bluuebunny/crossref_metadata_2025_split huggingface dataset:
Swimming performance of Bradyrhizobium diazoefficiens is an emergent property of its two flagellar systems
Authors: Quelas J. Ignacio , Althabegoiti M. Julia , Jimenez-Sanchez Celia , Melgarejo Augusto A. , Marconi Verónica I. , Mongiardini Elías J. , Trejo Sebastián A. , Mengucci Florencia , Ortega-Calvo José-Julio , Lodeiro Aníbal R. 
Published: April 2016

AbstractMany bacterial species use flagella for self-propulsion in aqueous media. In the soil, which is a complex and structured environment, water is found in microscopic channels where viscosity and water potential depend on the composition of the soil solution and the degree of soil water saturation. Therefore, the motility of soil bacteria might have special requirements. An important soil bacterial genus is Bradyrhizobium, with species that possess one flagellar system and others with two different flagellar systems. Among the latter is B. diazoefficiens, which may express its subpolar and lateral flagella simultaneously in liquid medium, although its swimming behaviour was not described yet. These two flagellar systems were observed here as functionally integrated in a swimming performance that emerged as an epistatic interaction between those appendages. In addition, each flagellum seemed engaged in a particular task that might be required for swimming oriented toward chemoattractants near the soil inner surfaces at viscosities that may occur after the loss of soil gravitational water. Because the possession of two flagellar systems is not general in Bradyrhizobium or in related genera that coexist in the same environment, there may be an adaptive tradeoff between energetic costs and ecological benefits among these different species.
Hormone replacement therapy and risk of atrial fibrillation in Taiwanese menopause women: A nationwide cohort study
Authors: Tsai Wei-Chung , Haung Yaw-Bin , Kuo Hsuan-Fu , Tang Wei-Hua , Hsu Po-Chao , Su Ho-Ming , Lin Tsung-Hsien , Chu Chih-Sheng , Jhuo Shih-Jie , Lee Kun-Tai , Sheu Sheng-Hsiung , Chen Chung-Yu , Wu Ming-Tsang , Lai Wen-Ter 
Published: April 2016

AbstractHormone replacement therapy (HRT) is associated with risk of vascular disease. The association between atrial fibrillation (AF), vascular events and different HRTs, including estradiol and conjugated equine estrogens (CEE), has been controversial in previous studies. Thus, we conducted a retrospective cohort study to investigate these associations. Female patients (>45 years old) first diagnosed with menopause were enrolled from National Health Insurance Research Dataset (1998–2008). Cox regression analysis estimated risk of new-onset AF, stroke and major adverse cardiac events (MACE) after exposure to estradiol or CEE. Of 5489 females (mean age = 55 years) enrolled, 1815 treated with estradiol and 3674 treated with CEE. Incidence per 103 person-years of AF, stroke and MACE in CEE vs estradiol patients was 2.23 vs. 0.92, 14.0 vs. 9.09 and 15.55 vs. 10.47. As compared with patients treated with estradiol, those treated with CEE had a significantly higher incidence of AF, stroke and MACE. The adjusted hazard ratios for each category were 1.96, 1.30 and 1.26, respectively. The significant results remained similar, even after use of propensity-score-matched strategy. In conclusion, CEE was associated with a higher risk of AF, stroke and MACE than estradiol in menopausal females. Further exploration of underlying mechanisms is necessary.
Image-based computational quantification and visualization of genetic alterations and tumour heterogeneity
Authors: Zhong Qing , Rüschoff Jan H. , Guo Tiannan , Gabrani Maria , Schüffler Peter J. , Rechsteiner Markus , Liu Yansheng , Fuchs Thomas J. , Rupp Niels J. , Fankhauser Christian , Buhmann Joachim M. , Perner Sven , Poyet Cédric , Blattner Miriam , Soldini Davide , Moch Holger , Rubin Mark A. , Noske Aurelia , Rüschoff Josef , Haffner Michael C. , Jochum Wolfram , Wild Peter J. 
Published: April 2016

AbstractRecent large-scale genome analyses of human tissue samples have uncovered a high degree of genetic alterations and tumour heterogeneity in most tumour entities, independent of morphological phenotypes and histopathological characteristics. Assessment of genetic copy-number variation (CNV) and tumour heterogeneity by fluorescencein situhybridization (ISH) provides additional tissue morphology at single-cell resolution, but it is labour intensive with limited throughput and high inter-observer variability. We present an integrative method combining bright-field dual-colour chromogenic and silver ISH assays with an image-based computational workflow (ISHProfiler), for accurate detection of molecular signals, high-throughput evaluation of CNV, expressive visualization of multi-level heterogeneity (cellular, inter- and intra-tumour heterogeneity), and objective quantification of heterogeneous genetic deletions (PTEN) and amplifications (19q12,HER2) in diverse human tumours (prostate, endometrial, ovarian and gastric), using various tissue sizes and different scanners, with unprecedented throughput and reproducibility.
PGC-1α Promotes Ureagenesis in Mouse Periportal Hepatocytes through SIRT3 and SIRT5 in Response to Glucagon
Authors: Li Lulu , Zhang Ping , Bao Zhengxi , Wang Tongxin , Liu Shuang , Huang Feiruo 
Published: April 2016

AbstractExcess ammonia is produced during fasting when amino acids are used for glucogenesis. Together with ureagenesis, glucogenesis occurs in periportal hepatocytes mediated mainly through the peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α). In vivo experiments showed that fasting strongly stimulated mice glucagon secretion, hepatic PGC-1α, sirtuin 3 (SIRT3) and sirtuin 5 (SIRT5) expression and ureagenesis enzymatic activity such as carbamoyl phosphate synthetase 1 (CPS1) and ornithine transcarbamoylase (OTC). Interestingly, 15N-labeled urea and 13C-labeled glucose production in wild-type mice were significantly increased compared with PGC-1α null mice by [15N,13C]alanine perfused liver. Glucagon significantly stimulated ureagenesis, expression of SIRT3, SIRT5 and the activities of CPS1 and OCT but did not stimulate PGC-1α silencing hepatocytes in mice periportal hepatocytes. Contrarily, PGC-1α overexpression significantly increased the expression of SIRT3, SIRT5 and the activities of CPS1 and OTC, but induced no significant changes in CPS1 and OTC expression. Morever, SIRT3 directly deacetylates and upregulates the activity of OTC, while SIRT5 deacetylates and stimulates the activity of CPS1. During fasting, PGC-1α facilitates ureagenesis in mouse periportal hepatocytes by deacetylating CPS1 and OTC modulated by mitochondrial deacetylase, SIRT3 and SIRT5. This mechanism may be relevant to ammonia detoxification and metabolic homeostasis in liver during fasting.
Imaging of Endogenous Metabolites of Plant Leaves by Mass Spectrometry Based on Laser Activated Electron Tunneling
Authors: Huang Lulu , Tang Xuemei , Zhang Wenyang , Jiang Ruowei , Chen Disong , Zhang Juan , Zhong Hongying 
Published: April 2016

AbstractA new mass spectrometric imaging approach based on laser activated electron tunneling (LAET) was described and applied to analysis of endogenous metabolites of plant leaves. LAET is an electron-directed soft ionization technique. Compressed thin films of semiconductor nanoparticles of bismuth cobalt zinc oxide were placed on the sample plate for proof-of-principle demonstration because they can not only absorb ultraviolet laser but also have high electron mobility. Upon laser irradiation, electrons are excited from valence bands to conduction bands. With appropriate kinetic energies, photoexcited electrons can tunnel away from the barrier and eventually be captured by charge deficient atoms present in neutral molecules. Resultant unpaired electron subsequently initiates specific chemical bond cleavage and generates ions that can be detected in negative ion mode of the mass spectrometer. LAET avoids the co-crystallization process of routinely used organic matrix materials with analyzes in MALDI (matrix assisted-laser desorption ionization) analysis. Thus uneven distribution of crystals with different sizes and shapes as well as background peaks in the low mass range resulting from matrix molecules is eliminated. Advantages of LAET imaging technique include not only improved spatial resolution but also photoelectron capture dissociation which produces predictable fragment ions.
Characterization of Discrete Phosphopantetheinyl Transferases in Streptomyces tsukubaensis L19 Unveils a Complicate Phosphopantetheinylation Network
Authors: Wang Yue-Yue , Zhang Xiao-Sheng , Luo Hong-Dou , Ren Ni-Ni , Jiang Xin-Hang , Jiang Hui , Li Yong-Quan 
Published: April 2016

AbstractPhosphopantetheinyl transferases (PPTases) play essential roles in both primary metabolisms and secondary metabolisms via post-translational modification of acyl carrier proteins (ACPs) and peptidyl carrier proteins (PCPs). In this study, an industrial FK506 producing strain Streptomyces tsukubaensis L19, together with Streptomyces avermitilis, was identified to contain the highest number (five) of discrete PPTases known among any species thus far examined. Characterization of the five PPTases in S. tsukubaensis L19 unveiled that stw ACP, an ACP in a type II PKS, was phosphopantetheinylated by three PPTases FKPPT1, FKPPT3 and FKACPS; sts FAS ACP, the ACP in fatty acid synthase (FAS), was phosphopantetheinylated by three PPTases FKPPT2, FKPPT3 and FKACPS; TcsA-ACP, an ACP involved in FK506 biosynthesis, was phosphopantetheinylated by two PPTases FKPPT3 and FKACPS; FkbP-PCP, an PCP involved in FK506 biosynthesis, was phosphopantetheinylated by all of these five PPTases FKPPT1-4 and FKACPS. Our results here indicate that the functions of these PPTases complement each other for ACPs/PCPs substrates, suggesting a complicate phosphopantetheinylation network in S. tsukubaensis L19. Engineering of these PPTases in S. tsukubaensis L19 resulted in a mutant strain that can improve FK506 production.
The Effects of Vitamin D-K-Calcium Co-Supplementation on Endocrine, Inflammation, and Oxidative Stress Biomarkers in Vitamin D-Deficient Women with Polycystic Ovary Syndrome: A Randomized, Double-Blind, Placebo-Controlled Trial
Authors: Razavi M. , Jamilian M. , Karamali M. , Bahmani F. , Aghadavod E. , Asemi Z. 
Published: April 2016

AbstractThe current study was conducted to assess the effects of vitamin D-K-calcium co-supplementation on endocrine, inflammation, and oxidative stress biomarkers in vitamin D-deficient women with polycystic ovary syndrome (PCOS). This randomized double-blind, placebo-controlled trial was performed on 60 vitamin D-deficient women diagnosed with PCOS aged 18–40 years old. Participants were randomly allocated into 2 groups to intake either 200 IU vitamin D, 90 μg vitamin K plus, 500 mg calcium supplements (n=30), or placebo (n=30) twice a day for 8 weeks. Endocrine, inflammation, and oxidative stress biomarkers were quantified at the beginning and the end of the study. After 8 weeks of intervention, compared with the placebo, vitamin D-K-calcium co-supplementation resulted in a significant reduction in serum-free testosterone (− 2.1±1.6 vs.+0.1±1.0 pg/ml, p<0.001) and dehydroepiandrosterone sulfate (DHEAS) levels (− 0.8±1.0 vs.−0.1±0.5 μg/ml, p=0.006). In addition, a significant increase in plasma total antioxidant capacity (TAC) (+ 75.7±126.1 vs.−80.4±242.8 mmol/l, p=0.005) and a significant difference in plasma malondialdehyde (MDA) concentrations (+ 0.03±0.6 vs.+1.4±2.4 μmol/l, p=0.005) was observed following the supplementation with vitamin D-K-calcium compared with the placebo. A trend toward a greater decrease in luteinizing hormone was observed in vitamin D-K-calcium co-supplement group compared to placebo group (− 7.0 vs.−1.2 IU/l, p=0.09). We did not find any significant effect of vitamin D-K-calcium co-supplementation on prolactin, follicle-stimulating hormone, 17-OH progesterone, inflammatory markers, and glutathione levels. Overall, vitamin D-K-calcium co-supplementation for 8 weeks among vitamin D-deficient women with PCOS had beneficial effects on serum DHEAS, free testosterone, plasma TAC, and MDA levels.
Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks
Authors: Wu Siqi , Joseph Antony , Hammonds Ann S. , Celniker Susan E. , Yu Bin , Frise Erwin 
Published: April 2016

SignificanceDespite the abundance of spatial gene expression data, extracting meaningful information to reveal how genes interact remains a challenge. We developed staNMF, a method that combines a powerful unsupervised learning algorithm, nonnegative matrix factorization (NMF), with a new stability criterion that selects the size of the dictionary or the set of principal patterns (PP). We demonstrate that PP give rise to a novel and concise representation of theDrosophilaembryonic spatial expression patterns and they correspond to biologically meaningful regions of theDrosophilaembryo. Furthermore, this new representation was used to automatically predict manual annotations, categorize gene expression patterns, and reconstruct the local gap gene network with high accuracy.
Characterisation of residual stresses in heat treated, high strength aluminium alloy extrusions
Authors: Olson M. D. , Robinson J. S. , Wimpory R. C. , Hill M. R. 
Published: April 2016

Residual stresses were measured in rectilinear aluminium bars quenched using an aqueous polyoxyethylene glycol (PAG) solution or cold-water. Residual stresses were measured with neutron diffraction and a superposition-based method using mechanical strain release measurements. Three orthogonal stress components were measured along two transverse lines using neutron diffraction. The longitudinal residual stresses were mapped over a transverse cross-section using the contour technique. A primary slice removal technique mapped three orthogonal residual stresses over a transverse cross-section in the PAG extrusion. Residual stresses were found to vary from biaxial compressive in the part boundaries to triaxial tensile in the interiors. There was close correlation between the neutron diffraction and mechanical strain release techniques. PAG quenching demonstrated lower residual stresses. This paper is part of a Themed Issue on Measurement, modelling and mitigation of residual stress.
Geographical location is a key component to effective breeding of clary sage (Salvia sclarea) for essential oil composition
Authors: Zutic Ivanka , Nitzan Nadav , Chaimovitsh David , Schechter Alona , Dudai Nativ 
Published: April 2016

Wild populations of Croatian clary sage (Salvia sclarea L.) were examined for variability to determine cultivation suitability in Croatia and Israel for breeding purposes. Phenotypic variability (coefficient of variation; %) was recorded for inflorescence weight (39.6%), inflorescence yield (52.8%), and essential oil yield (67.6%) when grown in Croatia. Associations were identified between inflorescence yield and essential oil yield (r = 0.9; P < 0.0001), inflorescence weight and inflorescence yield (r = 0.8; P < 0.0001), and inflorescence weight and inflorescence length (r = 0.6; P = 0.0056), suggesting that populations with elongated inflorescence are indirectly associated with higher essential oil yield. In Israel, the populations reached full bloom between the end of May and early June, corresponding on average to 397.5 days post planting. Linalyl acetate, linalool, α–terpineol, sclareol, and geranyl acetate were the leading essential oil components in both Croatia and Israel. The principal compounds in the oil were linalyl acetate (48.5%) and linalool (17.7%), signifying that the Croatian populations were of the linalool chemotype. A two-way ANOVA indicated an interaction between growing location (Croatia vs. Israel) and population for linalool (P = 0.02), α–terpineol (P = 0.007), and linalyl acetate (P = 0.09); evidence of an environmental effect on essential oil composition. The variation observed suggested that the wild population of clary sage in Croatia had the genetic heterogeneity essential for breeding. Nevertheless, the differences in essential oil composition between Croatia and Israel suggest that breeding efforts should be separately focused for each agriculture production system.
Plant community associations and complexes of associations in the Lithuanian seashore: retrospective on the studies and tragic fate of the botanist Dr Abromas Kisinas (1899-1945)
Authors: Naujalis Jonas Remigijus , Rimgailė-Voicik Radvilė 
Published: April 2016

The life and scientific activities and discoveries of Dr Abromas Kisinas (1899–1945, also appearing in the literature as Avraham, Abraham, Kisin or Kissin) are presented here for the first time. He was a botanist, a Lithuanian, a graduate of Vytautas Magnus University in Kaunas, a polyglot and a social figure. In 1936, Kisinas’ major phytosociological work “Plant Associations and Complexes of Associations in Lithuanian Seaside (without Klaipėda Region)” was published in the Works of Vytautas Magnus University Faculty of Mathematics and Natural Sciences. The publication was written in Lithuanian with a summary in German and summarized Kisinas’ PhD dissertation, which was defended in 1934 under the supervision of Prof. Constantin Regel. In his research, Kisinas applied ideas proposed by the Uppsala School of Phytosociology. For plant communities evaluation he used linear transects with 1 m2, 4 m2 and 16 m2 sampling squares. In a 15 km seashore range Kisinas determined 63 plant community associations and 26 sub-associations. The fate of this gifted scientist was tragic. In 1941 he and his family were deported to the Kaunas Ghetto. In 1945 Kisinas died at the Dachau concentration camp in Germany.
Excitation of external kink mode by trapped energetic particles
Authors: Guo S.C. , Xu X.Y. , Liu Y.Q. , Wang Z.R. 
Published: April 2016

Abstract
An unstable fishbone-like non-resonant external kink mode (FLEM) is numerically found to be driven by the precessional drift motion of trapped energetic particles (EPs) in both reversed-field pinch (RFP) and tokamak plasmas, even under the ideal wall boundary condition. In the presence of a sufficiently large fraction of trapped energetic ions in high beta plasmas, the FLEM instability may occur. The excitation condition is discussed in detail. The frequency of the FLEM is linked to the precessional drift frequency of EPs, and varies with the plasma flow speed. Therefore, it is usually much higher than that of the typical resistive wall mode (RWM). In general, the growth rate of FLEM does not depend on the wall resistivity. However, the wall position can significantly affect the mode’s property. The drift kinetic effects from thermal particles (mainly due to the transit resonance of passing particles) play a stabilizing role on FLEMs. In the presence of EPs, the FLEM and the RWM can co-exist or even couple to each other, depending on the plasma parameters. The FLEM instabilities in RFP and tokamaks have rather similar physics nature, although certain sub-dominant characters appear differently in the two configurations.
Efficacy of stereotactic body radiotherapy for hepatocellular carcinoma with portal vein tumor thrombosis/inferior vena cava tumor thrombosis: evaluation by comparison with conventional three-dimensional conformal radiotherapy
Authors: Matsuo Yoshiro , Yoshida Kenji , Nishimura Hideki , Ejima Yasuo , Miyawaki Daisuke , Uezono Haruka , Ishihara Takeaki , Mayahara Hiroshi , Fukumoto Takumi , Ku Yonson , Yamaguchi Masato , Sugimoto Koji , Sasaki Ryohei 
Published: April 2016

Abstract
This study aimed to evaluate the efficacy of stereotactic body radiotherapy (SBRT) compared with three-dimensional conformal radiotherapy (3DCRT). Forty-three patients with portal vein tumor thrombosis (PVTT)/inferior vena cava tumor thrombosis (IVCTT) treated with SBRT (27 with CyberKnife (CK) and 16 with TrueBeam (TB)) from April 2013 to December 2014, and 54 treated with 3DCRT from June 2008 to March 2013 were evaluated. Dosimetric parameters, response to radiotherapy (RT) and survival outcomes were compared in total SBRT vs. 3DCRT, CK vs. 3DCRT and TB vs. 3DCRT, respectively. The median biologically effective dose 10 (BED10) values in total SBRT, CK, TB and 3DCRT were 73.4 Gy10, 75.0 Gy10, 60.5 Gy10 and 58.5 Gy10, respectively (P &lt; 0.001 in total SBRT vs. 3DCRT, P &lt; 0.001 in CK vs. 3DCRT, P = 0.004 in TB vs. 3DCRT). The tumor response rates were 67%, 70%, 62% and 46%, respectively (P = 0.04, P = 0.04, P = 0.25). The 1-year overall survival rates were 49.3%, 56.7%, 38.1% and 29.3%, respectively (P = 0.02, P = 0.02, P = 0.30), and the 1-year local progression rates were 20.4%, 21.9%, 18.8% and 43.6%, respectively (P = 0.01, P = 0.04, P = 0.10). The use of SBRT made it possible to achieve a higher BED10 compared with the use of 3DCRT. Improvements in local control and survival were achieved in the CK group and the total SBRT group. Our results suggest that SBRT may have the potential to be the standard RT technique for the treatment of PVTT/IVCTT.
Three-dimensional relativistic MHD simulations of active galactic nuclei jets: magnetic kink instability and Fanaroff–Riley dichotomy
Authors: Tchekhovskoy Alexander , Bromberg Omer 
Published: April 2016

Abstract
Energy deposition by active galactic nuclei jets into the ambient medium can affect galaxy formation and evolution, the cooling of gas flows at the centres of galaxy clusters, and the growth of the supermassive black holes. However, the processes that couple jet power to the ambient medium and determine jet morphology are poorly understood. For instance, there is no agreement on the cause of the well-known Fanaroff–Riley (FR) morphological dichotomy of jets, with FRI jets being shorter and less stable than FRII jets. We carry out global 3D magnetohydrodynamic simulations of relativistic jets propagating through the ambient medium. We show that the flat density profiles of galactic cores slow down and collimate the jets, making them susceptible to the 3D magnetic kink instability. We obtain a critical power, which depends on the galaxy core mass and radius, below which jets become kink-unstable within the core, stall, and inflate cavities filled with relativistically hot plasma. Jets above the critical power stably escape the core and form powerful backflows. Thus, the kink instability controls the jet morphology and can lead to the FR dichotomy. The model-predicted dependence of the critical power on the galaxy optical luminosity agrees well with observations.