bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of 34-year continuous fertilization on the SOC physical fractions and its chemical composition in a Vertisol
Authors: Guo Zichun , Zhang Zhongbin , Zhou Hu , Wang Daozhong , Peng Xinhua 
Published: February 2019

AbstractReports regarding the effects of long-term organic and inorganic fertilization on the quantity and quality of soil organic carbon (SOC), particularly in Vertisols, are scarce. In this study, we combined SOC physical fractionation with 13C NMR spectroscopy technology to investigate the effect of 34 years of continuous fertilization on the SOC physical fractions and its chemical composition of 0–20 cm soil layer in a Vertisol. This study consisted of six treatments: no fertilization (control), chemical nitrogen, phosphorus and potassium fertilizers (NPK), low and high amounts of straw with chemical fertilizers (NPKLS and NPKHS), and pig or cattle manure with chemical fertilizers (NPKPM and NPKCM). Over 34 years of continuous fertilization, the SOC sequestration rate was from 0.08 Mg C ha−1 yr−1 in the control treatment to 0.66 Mg C ha−1 yr−1 in the NPKCM treatment, which was linearly related with the C input (P < 0.01). Of the five SOC physical fractions, two silt plus clay fractions (S + C_M, S + C_mM) dominated 74–92% of SOC, while three POM fractions (cPOM fPOM and iPOM) were only 8–26%. The two manure application treatments significantly increased all the SOC physical fractions except for the silt plus clay fraction within macroaggregates (S + C_M) compared with NPK treatment (P < 0.05), which was dependent on the larger amount of C input. Also, the two manure application treatments increased the levels of alkyl C and aromatic C but decreased O-alkyl C (P < 0.05), whereas the straw application (NPKLS and NPKHS) had no impact on the C functional groups (P > 0.05). Overall, the combination of animal manure with inorganic fertilization could enhance the SOC sequestration and alter its quantity and quality in Vertisols.
Premobilization of CD133+ cells by granulocyte colony- stimulating factor attenuates ischemic acute kidney injury induced by cardiopulmonary bypass
Authors: Li Xiaoqiang , Wan Qin , Min Jie , Duan Linjia , Liu Jin 
Published: February 2019

AbstractIschemic acute kidney injury (IAKI) is a common but severe complication after a cardiopulmonary bypass (CPB). Multiple studies have demonstrated that peripheral CD133+ or differentiated cells are able to home and repair the damaged tissues, but the number of available CD133+ cells is limited, and no efficient method published previously to mobilize them immediately. We analyzed the relationship between CD133+ cells and renal function in CPB patients, in addition, the efficacy of granulocyte colony-stimulating factor (G-CSF) pre-mobilized CD133+ cells in treating of mouse IAKI model have been investigated. In the clinical study, the prospective cohort study analyzed the correlation between BUN/Crea level and the peripheral CD133+ cell numbers. CPB was associated with postoperative renal dysfunction. The significant negative correlation was observed between patients’ Crea and CD133+ cells (P < 0.05). The proposed mechanism studies were performed on the mouse IAKI model. The experimental mice were treated by G-CSF to mobilize CD133+ cells before implementing CPB. Data on cell count, inflammatory index, renal function/injury, and CD133+ cell mobilization were analyzed. The result demonstrated that pretreatment by G-CSF resulted in tremendous increase in the number of mouse peripheral blood and renal CD133+ cells, significantly reduces renal tissue inflammation and dramatically improves the renal function after CPB. In summary, we concluded that premobilization of CD133+ cells abated CPB induced IAKI, by promoting both repairing damaged epithelium and by its anti-inflammatory activity. Our findings stress the remarkable applications of CD133+ or differentiated cells-based therapies for potential preventing ischemic acute kidney injury.
Asymmetric independence modeling identifies novel gene-environment interactions
Authors: Yu Guoqiang , Miller David J. , Wu Chiung-Ting , Hoffman Eric P. , Liu Chunyu , Herrington David M. , Wang Yue 
Published: February 2019

AbstractMost genetic or environmental factors work together in determining complex disease risk. Detecting gene-environment interactions may allow us to elucidate novel and targetable molecular mechanisms on how environmental exposures modify genetic effects. Unfortunately, standard logistic regression (LR) assumes a convenient mathematical structure for the null hypothesis that however results in both poor detection power and type 1 error, and is also susceptible to missing factor, imperfect surrogate, and disease heterogeneity confounding effects. Here we describe a new baseline framework, the asymmetric independence model (AIM) in case-control studies, and provide mathematical proofs and simulation studies verifying its validity across a wide range of conditions. We show that AIM mathematically preserves the asymmetric nature of maintaining health versus acquiring a disease, unlike LR, and thus is more powerful and robust to detect synergistic interactions. We present examples from four clinically discrete domains where AIM identified interactions that were previously either inconsistent or recognized with less statistical certainty.
Cardiac molecular pathways influenced by doxorubicin treatment in mice
Authors: Bulten Ben F. , Sollini Martina , Boni Roberto , Massri Katrin , de Geus-Oei Lioe-Fee , van Laarhoven Hanneke W. M. , Slart Riemer H. J. A. , Erba Paola A. 
Published: February 2019

AbstractDoxorubicin (DOX) is a potent chemotherapeutic with distinct cardiotoxic properties. Understanding the underlying cardiotoxic mechanisms on a molecular level would enable the early detection of cardiotoxicity and implementation of prophylactic treatment. Our goal was to map the patterns of different radiopharmaceuticals as surrogate markers of specific metabolic pathways induced by chemotherapy. Therefore, cardiac distribution of 99mTc-sestamibi, 99mTc-Annexin V, 99mTc-glucaric acid and [18F]FDG and cardiac expression of Bcl-2, caspase-3 and -8, TUNEL, HIF-1α, and p53 were assessed in response to DOX exposure in mice. A total of 80 mice (64 treated, 16 controls) were evaluated. All radiopharmaceuticals showed significantly increased uptake compared to controls, with peak cardiac uptake after one (99mTc-Annexin V), two (99mTc-sestamibi), three ([18F]FDG), or four (99mTc-glucaric acid) cycles of DOX. Strong correlations (p < 0.01) were observed between 99mTc-Annexin V, caspase 3 and 8, and TUNEL, and between [18F]FDG and HIF-1α. This suggests that the cardiac DOX response starts with apoptosis at low exposure levels, as indicated by 99mTc-Annexin V and histological apoptosis markers. Late process membrane disintegration can possibly be detected by 99mTc-sestamibi and 99mTc-glucaric acid. [18F]FDG signifies an early adaptive response to DOX, which can be further exploited clinically in the near future.
Decoupling a novel Trichormus variabilis-Synechocystis sp. interaction to boost phycoremediation
Authors: Abedi Sepideh , Astaraei Fatemeh Razi , Ghobadian Barat , Tavakoli Omid , Jalili Hassan , Greenwell H. Christopher , Cummins Ian , Chivasa Stephen 
Published: February 2019

AbstractTo conserve freshwater resources, domestic and industrial wastewater is recycled. Algal systems have emerged as an efficient, low-cost option for treatment (phycoremediation) of nutrient-rich wastewater and environmental protection. However, industrial wastewater may contain growth inhibitory compounds precluding algal use in phycoremediation. Therefore, extremophyte strains, which thrive in hostile environments, are sought-after. Here, we isolated such an alga - a strain of Synechocystis sp. we found to be capable of switching from commensal exploitation of the nitrogen-fixing Trichormus variabilis, for survival in nitrogen-deficient environments, to free-living growth in nitrate abundance. In nitrogen depletion, the cells are tethered to polysaccharide capsules of T. variabilis using nanotubular structures, presumably for nitrate acquisition. The composite culture failed to establish in industrial/domestic waste effluent. However, gradual exposure to increasing wastewater strength over time untethered Synechocystis cells and killed off T. variabilis. This switched the culture to a stress-acclimated monoculture of Synechocystis sp., which rapidly grew and flourished in wastewater, with ammonium and phosphate removal efficiencies of 99.4% and 97.5%, respectively. Therefore, this strain of Synechocystis sp. shows great promise for use in phycoremediation, with potential to rapidly generate biomass that can find use as a green feedstock for valuable bio-products in industrial applications.
Deciphering Z-scheme Charge Transfer Dynamics in Heterostructure NiFe-LDH/N-rGO/g-C3N4 Nanocomposite for Photocatalytic Pollutant Removal and Water Splitting Reactions
Authors: Nayak Susanginee , Parida K. M. 
Published: February 2019

AbstractA series of heterostructure NiFe LDH/N-rGO/g-C3N4 nanocomposite were fabricated by combining calcinations-electrostatic self-assembly and hydrothermal steps. In this method, negatively charged N-rGO was electrostaticaly bonded to the self-assembled interface of n-n type g-C3N4/NiFe LDH hybrid. XRD and AFM results revealed successful formation of heterostructure nanocomposite due to the coupling effect of exfoliated NiFe LDH nanosheets with N-rGO and g-C3N4. Among the as synthesized heterostructure, CNNG3LDH performed superior photocatalytic activities towards 95 and 72% mineralization of RhB and phenol. Furthermore, CNNG3LDH could achieve the highest photocatalytic H2 evolution rate of 2508 μmolg−12h−1 and O2 evolution rate of 1280 μmolg−12h−1 under visible light irradiation. The CNNG3LDH possess lowest PL intensity, reduced arc of the Nyquist plot (43.8 Ώ) and highest photocurrent density (−0.97 mA cm−2) which revealed effective charge separation for superior photocatalytic activities. TRPL spectral results reveal the synergistic effect of layered component in CNNG3LDH for achievable higher life time of excitons of ~16.52 ns. In addition, N-rGO mediator based Z-scheme charge transfer mechanisms in CNNG3LDH were verified by the ESR and TA-PL studies. Enriched oxygen vacancy type defects in NiFe LDH and N-rGO mediated Z-scheme charge transfer mechanistic path strongly manifest the superior photocatalytic activities of the heterostructure materials.
Consequences of prenatal exposure to valproic acid in the socially monogamous prairie voles
Authors: Sailer L. , Duclot F. , Wang Z. , Kabbaj M. 
Published: February 2019

AbstractEnvironmental risk factors contribute to autism spectrum disorders (ASD) etiology. In particular, prenatal exposure to the highly teratogenic anticonvulsant valproic acid (VPA) significantly increases ASD prevalence. Although significant discoveries on the embryopathology of VPA have been reported, its effects on the ability to form enduring social attachment—characteristic of ASD but uncommonly displayed by rats and mice—remains unknown. We aimed to examine the effects of prenatal VPA exposure in the social, monogamous prairie voles (Microtus ochrogaster). Compared to prenatal vehicle-exposed controls, prenatal VPA-exposed prairie voles had lower body weight throughout postnatal development, engaged in fewer social affiliative behaviors in a familial context, exhibited less social interactions with novel conspecifics, and showed enhanced anxiety-like behavior. Along these behavioral deficits, prenatal VPA exposure downregulated prefrontal cortex vasopressin receptor (V1aR) and methyl CpG-binding protein 2 (MeCP2) mRNA expression, but did not alter spine density in adults. Remarkably, adult social bonding behaviors, such as partner preference formation and selective aggression, were not disrupted by prenatal VPA exposure. Collectively, these studies suggest that, in this animal model, VPA alters only certain behavioral domains such as sex-naive anxiety and affiliative behaviors, but does not alter other domains such as social bonding with opposite sex individuals.
Polyacrylamide injection matrix for serial femtosecond crystallography
Authors: Park Jaehyun , Park Sehan , Kim Jangwoo , Park Gisu , Cho Yunje , Nam Ki Hyun 
Published: February 2019

AbstractSerial femtosecond crystallography (SFX) provides opportunities to observe the dynamics of macromolecules without causing radiation damage at room temperature. Although SFX provides a biologically more reliable crystal structure than provided by the existing synchrotron sources, there are limitations due to the consumption of many crystal samples. A viscous medium as a carrier matrix reduces the flow rate of the crystal sample from the injector, thereby dramatically reducing sample consumption. However, the currently available media cannot be applied to specific crystal samples owing to reactions between the viscous medium and crystal sample. The discovery and characterisation of a new delivery medium for SFX can further expand its use. Herein, we report the preparation of a polyacrylamide (PAM) injection matrix to determine the crystal structure with an X-ray free-electron laser. We obtained 11,936 and 22,213 indexed images using 0.5 mg lysozyme and 1.0 mg thermolysin, respectively. We determined the crystal structures of lysozyme and thermolysin delivered in PAM at 1.7 Å and 1.8 Å resolutions. The maximum background scattering from PAM was lower than monoolein, a commonly used viscous medium. Our results show that PAM can be used as a sample delivery media in SFX studies.
Removing the no-analogue bias in modern accelerated tree growth leads to stronger medieval drought
Authors: Scharnweber Tobias , Heußner Karl-Uwe , Smiljanic Marko , Heinrich Ingo , van der Maaten-Theunissen Marieke , van der Maaten Ernst , Struwe Thomas , Buras Allan , Wilmking Martin 
Published: February 2019

AbstractIn many parts of the world, especially in the temperate regions of Europe and North-America, accelerated tree growth rates have been observed over the last decades. This widespread phenomenon is presumably caused by a combination of factors like atmospheric fertilization or changes in forest structure and/or management. If not properly acknowledged in the calibration of tree-ring based climate reconstructions, considerable bias concerning amplitudes and trends of reconstructed climatic parameters might emerge or low frequency information is lost. Here we present a simple but effective, data-driven approach to remove the recent non-climatic growth increase in tree-ring data. Accounting for the no-analogue calibration problem, a new hydroclimatic reconstruction for northern-central Europe revealed considerably drier conditions during the medieval climate anomaly (MCA) compared with standard reconstruction methods and other existing reconstructions. This demonstrates the necessity to account for fertilization effects in modern tree-ring data from affected regions before calibrating reconstruction models, to avoid biased results.
Comparison between chronic hepatitis B patients with untreated immune-tolerant phase vs. those with virological response by antivirals
Authors: Lee Hye Won , Kim Seung Up , Baatarkhuu Oidov , Park Jun Yong , Kim Do Young , Ahn Sang Hoon , Han Kwang-Hyub , Kim Beom Kyung 
Published: February 2019

AbstractRoutine nucleos(t)ide analogs (NUCs) have not yet been recommended for patients with immune-tolerant (IT) phase in chronic hepatitis B virus (HBV) infection. We aimed to evaluate prognosis of patients in untreated IT-phase (UIT group), compared to those in immune-active phase who achieved virological response by NUCs according to guidelines (VR group). Between 2006 and 2012, patients in UIT or VR groups were included. Cumulative risks of HCC and liver-related events (LREs) development were assessed. Furthermore, propensity-score was calculated based upon age, gender, diabetes and liver stiffness. UIT group (n = 126) showed younger age, lower proportion of male gender and lower LS than VR group (n = 641). UIT group had similar 10-year cumulative risks of HCC (2.7% vs. 2.9%, p = 0.704) and LRE (4.6% vs. 6.1%, p = 0.903) development, compared to VR group. When we re-defined UIT group by the lower ALT cut-offs, 10-year cumulative risks of HCC and LRE development were 2.9% and 4.8%, respectively. Using propensity-score matching and inverse probability treatment weighting analysis, similar results were reproduced. UIT group consistently had similar prognosis compared to VR group. Therefore, further large-scale prospective studies in order to verify rationales of routine NUCs in UIT group are still required.
Emergence of Two different recombinant PRRSV strains with low neutralizing antibody susceptibility in China
Authors: Han Guangwei , Xu Huiling , Wang Kexiong , He Fang 
Published: February 2019

AbstractPRRSV causes major economic loss in global swine industry. 41 of 131 (31.29%) tissue samples collected from pig farms in central and east China from 2016 to 2017 were confirmed as PRRSV positive in RT-PCR. Base on phylogenetic analysis for ORF5 and ORF6, 3 isolates closely related to QYYZ strain form a new subgroup IV, while 3 other ones were clustered into subgroup III, represented by NADC30. Numerous amino acid substitutions involved in viral neutralization susceptibility were identified in GP5 among these isolates. Two emerging PRRSV strains (ZJnb16-2, SDbz16-2) were successfully isolated and sequenced. ZJnb16-2 was identified as a recombinant virus between strain QYYZ and JXA1 while SDbz16-2 was an inter-subgenotype recombinant virus of strains NADC30 and JXA1. As shown in the pathogenicity evaluation in piglets, ZJnb16-2 is highly pathogenic while SDbz16-2 is mild. Hyper-immune sera against major vaccine strains HUN4-F112 and JK-100 failed to neutralize either ZJnb16-2 or SDbz16-2. Only 0.8–2.0% of pig serum samples which were confirmed as PRRSV-positive with commercial ELISA kits presented neutralization reactivity against either ZJnb16-2 or SDbz16-2. The study confirmed that the viral genomic recombination contributes to the emergence of new pathogenic PRRSVs in China, which may escape from the protective immunity elicited by the conventional vaccines, highlighting the necessity in updates of vaccine strains and the need for a universal vaccine against PRRSV.
Transcriptomic studies and assessment of Yersinia pestis reference genes in various conditions
Authors: Koch Lionel , Poyot Thomas , Schnetterle Marine , Guillier Sophie , Soulé Estelle , Nolent Flora , Gorgé Olivier , Neulat-Ripoll Fabienne , Valade Eric , Sebbane Florent , Biot Fabrice 
Published: February 2019

AbstractReverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a very sensitive widespread technique considered as the gold standard to explore transcriptional variations. While a particular methodology has to be followed to provide accurate results many published studies are likely to misinterpret results due to lack of minimal quality requirements. Yersinia pestis is a highly pathogenic bacterium responsible for plague. It has been used to propose a ready-to-use and complete approach to mitigate the risk of technical biases in transcriptomic studies. The selection of suitable reference genes (RGs) among 29 candidates was performed using four different methods (GeNorm, NormFinder, BestKeeper and the Delta-Ct method). An overall comprehensive ranking revealed that 12 following candidate RGs are suitable for accurate normalization: gmk, proC, fabD, rpoD, nadB, rho, thrA, ribD, mutL, rpoB, adk and tmk. Some frequently used genes like 16S RNA had even been found as unsuitable to study Y. pestis. This methodology allowed us to demonstrate, under different temperatures and states of growth, significant transcriptional changes of six efflux pumps genes involved in physiological aspects as antimicrobial resistance or virulence. Previous transcriptomic studies done under comparable conditions had not been able to highlight these transcriptional modifications. These results highlight the importance of validating RGs prior to the normalization of transcriptional expression levels of targeted genes. This accurate methodology can be extended to any gene of interest in Y. pestis. More generally, the same workflow can be applied to identify and validate appropriate RGs in other bacteria to study transcriptional variations.
The parental co-immunization hypothesis: An observational competing risks analysis
Authors: Portela Miguel , Schweinzer Paul 
Published: February 2019

AbstractThe main interest of this study is the hypothesis that contact with small children may be beneficial for the parents’ later health and mortality (because of changes in their immune system). For this purpose, we document the relationship of a set of individual characteristics—including parenthood and marital state—and socioeconomic status with an individual’s cause of death. Using a novel and rich data set made available by the Office for National Statistics Longitudinal Study (ONS-LS), which follows 1% of the population of England and Wales along five census waves 1971, 1981, 1991, 2001, and 2011, our competing risks analysis yields several striking results: (1) Females with children have a 72.5% reduced risk of dying of cancer compared to childless females (for childless females of age 70, this corresponds to a risk of dying of cancer of 1.3% compared to a risk of about 1.3 × 0.275 = 0.4% for females with children). (2) Males have a 171% increased chance of dying of cancer when they are married (e.g., a baseline probability of 1.2% when 75 year old) compared to unmarried males. (3) Females with children have only a 34% risk of dying of heart disease (corresponding to a conditional probability of 0.3% when aged 65) relative to females without children and (4) a 53% chance of dying of infections (i.e., 0.1% at 65 years of age) compared to the risk for females without children. (5) At the same age, married men have an increased expectation of 123% of dying of heart disease (corresponding to an expected death probability of 0.7%) compared to unmarried men. (6) High income and house ownership is always associated with higher survival but less so than having children. While these results document a relationship between the presence of children and mortality, the specific transmission mechanisms remain unclear and we cannot make causality assertions.
Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes
Authors: Czech Andreas , Konarev Petr V. , Goebel Ingrid , Svergun Dmitri I. , Wills Peter R. , Ignatova Zoya 
Published: February 2019

AbstractMisfolding and aggregation of prion protein (PrP) causes neurodegenerative diseases like Creutzfeldt-Jakob disease (CJD) and scrapie. Besides the consensus that spontaneous conversion of normal cellular PrPCinto misfolded and aggregating PrPScis the central event in prion disease, an alternative hypothesis suggests the generation of pathological PrPScby rare translational frameshifting events in the octa-repeat domain of the PrP mRNA. Ribosomal frameshifting most commonly relies on a slippery site and an adjacent stable RNA structure to stall translating ribosome. Hence, it is crucial to unravel the secondary structure of the octa-repeat domain of PrP mRNA. Each of the five octa-repeats contains a motif (GGCGGUGGUGGCUGGG) which alonein vitroforms a G-quadruplex. Since the propensity of mRNA to form secondary structure depends on the sequence context, we set to determine the structure of the complete octa-repeat region. We assessed the structure of full-length octa-repeat domain of PrP mRNA using dynamic light scattering (DLS), small angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy and selective 2′-hydroxyl acylation analysis by primer extension (SHAPE). Our data show that the PrP octa-repeat mRNA forms stable A-helical hairpins with no evidence of G-quadruplex structure even in the presence of G-quadruplex stabilizing agents.