bluuebunny/crossref_metadata_2025_split huggingface dataset:
Domestication and ontogeny effects on the stress response in young chickens (Gallus gallus)
Authors: Ericsson Maria , Jensen Per 
Published: October 2016

AbstractDomestication is thought to increase stress tolerance. The connection between stressor exposure, glucocorticoids and behavioural responses has been studied in adults, where domestication effects are evident. Early stress exposure may induce detrimental effects both in short-and long term. Previous research has reported a lack of glucocorticoid response in newly hatched chickens (Gallus gallus), whereas others have found opposite results. Hence it remains unclear whether the HPA-axis is functional from hatch, and if domestication has affected the early post-hatch ontogeny of the stress response. Our aims were to investigate the early ontogeny of the HPA-axis and characterize behavioural and hormonal stress responses in ancestral Red Junglefowl and in two domestic layer strains. Plasma corticosteone and behavioural responses before and after physical restraint was measured on day one, nine, 16 and 23 post hatch. The results showed significant increases of corticosterone after stress in all three breeds at all the different ages. The HPA-response decreased with age and was lower in Red Junglefowl. Behavioural responses also decreased with age, and tended to be stronger in Red Junglefowl. In summary, the HPA-axis is reactive from day one, and domestication may have affected its development and reactivity, alongside with related behaviour responses.
Structural elucidation of estrus urinary lipocalin protein (EULP) and evaluating binding affinity with pheromones using molecular docking and fluorescence study
Authors: Rajesh Durairaj , Muthukumar Subramanian , Saibaba Ganesan , Siva Durairaj , Akbarsha Mohammad Abdulkader , Gulyás Balázs , Padmanabhan Parasuraman , Archunan Govindaraju 
Published: October 2016

AbstractTransportation of pheromones bound with carrier proteins belonging to lipocalin superfamily is known to prolong chemo-signal communication between individuals belonging to the same species. Members of lipocalin family (MLF) proteins have three structurally conserved motifs for delivery of hydrophobic molecules to the specific recognizer. However, computational analyses are critically required to validate and emphasize the sequence and structural annotation of MLF. This study focused to elucidate the evolution, structural documentation, stability and binding efficiency of estrus urinary lipocalin protein (EULP) with endogenous pheromones adopting in-silico and fluorescence study. The results revealed that: (i) EULP perhaps originated from fatty acid binding protein (FABP) revealed in evolutionary analysis; (ii) Dynamic simulation study shows that EULP is highly stable at below 0.45 Å of root mean square deviation (RMSD); (iii) Docking evaluation shows that EULP has higher binding energy with farnesol and 2-iso-butyl-3-methoxypyrazine (IBMP) than 2-naphthol; and (iv) Competitive binding and quenching assay revealed that purified EULP has good binding interaction with farnesol. Both, In-silico and experimental studies showed that EULP is an efficient binding partner to pheromones. The present study provides impetus to create a point mutation for increasing longevity of EULP to develop pheromone trap for rodent pest management.
Cattle encephalon glycoside and ignotin reduced white matter injury and prevented post-hemorrhagic hydrocephalus in a rat model of intracerebral hemorrhage
Authors: Li Rongwei , Ma Kang , Zhao Hengli , Feng Zhou , Yang Yang , Ge Hongfei , Zhang Xuan , Tang Jun , Yin Yi , Liu Xin , Tan Liang , Feng Hua 
Published: October 2016

AbstractThe morbidity, mortality, and disability associated with intraventricular hemorrhage (IVH) secondary to intracerebral hemorrhage (ICH) represent a global burden. To date, there is no effective therapy for ICH other than supportive care. In this study, we assessed the neuroprotective effects of Cattle encephalon glycoside and ignotin (CEGI) injection in a rat model of ICH with ventricular extension (IVH/ICH). The IVH/ICH rat model was induced via injection of type IV collagenase in the caudate nucleus of Sprague-Dawley rats. The experimental animals were randomized to receive CEGI, monosialotetrahexosyl ganglioside (GM-1), or normal saline. The modified Garcia scale, corner turn test, immunofluorescence staining for myelin basic protein (MBP) and microtubule associated protein 2 (MAP-2), transmission electron microscopy (TEM), and magnetic resonance imaging were employed to evaluate the neuroprotective effect of CEGI in the IVH/ICH rat model. CEGI treatment significantly alleviated the neurobehavioral dysfunction, reduced the lateral ventricular enlargement, promoted hematoma absorption, effectively up-regulated MBP/MAP-2 expression, and ameliorated white matter fiber damage post-ICH induction. Our results demonstrate that CEGI has significant neuroprotective effects in a rat model of IVH/ICH. Therefore, it can be used as a candidate drug for the clinical treatment of IVH/ICH.
Expression of varied GFPs in Saccharomyces cerevisiae: codon optimization yields stronger than expected expression and fluorescence intensity
Authors: Kaishima Misato , Ishii Jun , Matsuno Toshihide , Fukuda Nobuo , Kondo Akihiko 
Published: October 2016

AbstractGreen fluorescent protein (GFP), which was originally isolated from jellyfish, is a widely used tool in biological research, and homologs from other organisms are available. However, researchers must determine which GFP is the most suitable for a specific host. Here, we expressed GFPs from several sources in codon-optimized and non-codon-optimized forms in the yeast Saccharomyces cerevisiae, which represents an ideal eukaryotic model. Surprisingly, codon-optimized mWasabi and mNeonGreen, which are typically the brightest GFPs, emitted less green fluorescence than did the other five codon-optimized GFPs tested in S. cerevisiae. Further, commercially available GFPs that have been optimized for mammalian codon usage (e.g., EGFP, AcGFP1 and TagGFP2) unexpectedly exhibited extremely low expression levels in S. cerevisiae. In contrast, codon-optimization of the GFPs for S. cerevisiae markedly increased their expression levels, and the fluorescence intensity of the cells increased by a maximum of 101-fold. Among the tested GFPs, the codon-optimized monomeric mUkG1 from soft coral showed the highest levels of both expression and fluorescence. Finally, the expression of this protein as a fusion-tagged protein successfully improved the reporting system’s ability to sense signal transduction and protein–protein interactions in S. cerevisiae and increased the detection rates of target cells using flow cytometry.
Super-resolution imaging of fluorescently labeled, endogenous RNA Polymerase II in living cells with CRISPR/Cas9-mediated gene editing
Authors: Cho Won-Ki , Jayanth Namrata , Mullen Susan , Tan Tzer Han , Jung Yoon J. , Cissé Ibrahim I. 
Published: October 2016

AbstractLive cell imaging of mammalian RNA polymerase II (Pol II) has previously relied on random insertions of exogenous, mutant Pol II coupled with the degradation of endogenous Pol II using a toxin, α-amanitin. Therefore, it has been unclear whether over-expression of labeled Pol II under an exogenous promoter may have played a role in reported Pol II dynamics in vivo. Here we label the endogenous Pol II in mouse embryonic fibroblast (MEF) cells using the CRISPR/Cas9 gene editing system. Using single-molecule based super-resolution imaging in the living cells, we captured endogenous Pol II clusters. Consistent with previous studies, we observed that Pol II clusters were short-lived (cluster lifetime ~8 s) in living cells. Moreover, dynamic responses to serum-stimulation, and drug-mediated transcription inhibition were all in agreement with previous observations in the exogenous Pol II MEF cell line. Our findings suggest that previous exogenously tagged Pol II faithfully recapitulated the endogenous polymerase clustering dynamics in living cells, and our approach may in principle be used to directly label transcription factors for live cell imaging.
Renoprotective Effects of Metformin are Independent of Organic Cation Transporters 1 & 2 and AMP-activated Protein Kinase in the Kidney
Authors: Christensen Michael , Jensen Jonas B. , Jakobsen Steen , Jessen Niels , Frøkiær Jørgen , Kemp Bruce E. , Marciszyn Allison L. , Li Hui , Pastor-Soler Núria M. , Hallows Kenneth R. , Nørregaard Rikke 
Published: October 2016

AbstractThe type-2 diabetes drug metformin has proven to have protective effects in several renal disease models. Here, we investigated the protective effects in a 3-day unilateral ureteral obstruction (3dUUO) mouse model. Compared with controls, ureteral obstructed animals displayed increased tubular damage and inflammation. Metformin treatment attenuated inflammation, increased the anti-oxidative response and decreased tubular damage. Hepatic metformin uptake depends on the expression of organic cation transporters (OCTs). To test whether the effects of metformin in the kidney are dependent on these transporters, we tested metformin treatment in OCT1/2−/− mice. Even though exposure of metformin in the kidney was severely decreased in OCT1/2−/− mice when evaluated with [11C]-Metformin and PET/MRI, we found that the protective effects of metformin were OCT1/2 independent when tested in this model. AMP-activated protein kinase (AMPK) has been suggested as a key mediator of the effects of metformin. When using an AMPK-β1 KO mouse model, the protective effects of metformin still occurred in the 3dUUO model. In conclusion, these results show that metformin has a beneficial effect in early stages of renal disease induced by 3dUUO. Furthermore, these effects appear to be independent of the expression of OCT1/2 and AMPK-β1, the most abundant AMPK-β isoform in the kidney.
Phylogenetic and functional potential links pH and N2O emissions in pasture soils
Authors: Samad Md Sainur , Biswas Ambarish , Bakken Lars R. , Clough Timothy J. , de Klein Cecile A. M. , Richards Karl G. , Lanigan Gary J. , Morales Sergio E. 
Published: October 2016

AbstractDenitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2.
Modeling analysis of secondary inorganic aerosols over China: pollution characteristics, and meteorological and dust impacts
Authors: Fu Xiao , Wang Shuxiao , Chang Xing , Cai Siyi , Xing Jia , Hao Jiming 
Published: October 2016

AbstractSecondary inorganic aerosols (SIA) are the predominant components of fine particulate matter (PM2.5) and have significant impacts on air quality, human health, and climate change. In this study, the Community Multiscale Air Quality modeling system (CMAQ) was modified to incorporate SO2heterogeneous reactions on the surface of dust particles. The revised model was then used to simulate the spatiotemporal characteristics of SIA over China and analyze the impacts of meteorological factors and dust on SIA formation. Including the effects of dust improved model performance for the simulation of SIA concentrations, particularly for sulfate. The simulated annual SIA concentration in China was approximately 10.1 μg/m3on domain average, with strong seasonal variation: highest in winter and lowest in summer. High SIA concentrations were concentrated in developed regions with high precursor emissions, such as the North China Plain, Yangtze River Delta, Sichuan Basin, and Pearl River Delta. Strong correlations between meteorological factors and SIA pollution levels suggested that heterogeneous reactions under high humidity played an important role on SIA formation, particularly during severe haze pollution periods. Acting as surfaces for heterogeneous reactions, dust particles significantly affected sulfate formation, suggesting the importance of reducing dust emissions for controlling SIA and PM2.5pollution.
Angiotensin II type-1 receptor (AT1R) regulates expansion, differentiation, and functional capacity of antigen-specific CD8+ T cells
Authors: Silva-Filho João Luiz , Caruso-Neves Celso , Pinheiro Ana Acacia Sá 
Published: October 2016

AbstractAngiotensin II (Ang II) and its receptor AT1 (AT1R), an important effector axis of renin-angiotensin system (RAS), have been demonstrated to regulate T-cell responses. However, these studies characterized Ang II and AT1R effects using pharmacological tools, which do not target only Ang II/AT1R axis. The specific role of AT1R expressed by antigen-specific CD8+ T cells is unknown. Then we immunized transgenic mice expressing a T-cell receptor specific for SIINFEKL epitope (OT-I mice) with sporozoites of the rodent malaria parasite Plasmodium berghei expressing the cytotoxic epitope SIINFEKL. Early priming events after immunization were not affected but the expansion and contraction of AT1R-deficient (AT1R−/−) OT-I cells was decreased. Moreover, they seemed more activated, express higher levels of CTLA-4, PD-1, LAG-3, and have decreased functional capacity during the effector phase. Memory AT1R−/− OT-I cells exhibited higher IL-7Rα expression, activation, and exhaustion phenotypes but less cytotoxic capacity. Importantly, AT1R−/− OT-I cells show better control of blood parasitemia burden and ameliorate mice survival during lethal disease induced by blood-stage malaria. Our study reveals that AT1R in antigen-specific CD8+ T cells regulates expansion, differentiation, and function during effector and memory phases of the response against Plasmodium, which could apply to different infectious agents.
Diagnostic Value and Surgical Implications of the 3D DW-SSFP MRI On the Management of Patients with Brachial Plexus Injuries
Authors: Qin Ben-Gang , Yang Jian-Tao , Yang Yi , Wang Hong-Gang , Fu Guo , Gu Li-Qiang , Li Ping , Zhu Qing-Tang , Liu Xiao-Lin , Zhu Jia-Kai 
Published: October 2016

AbstractThree-dimensional diffusion-weighted steady-state free precession (3D DW-SSFP) of high-resolution magnetic resonance has emerged as a promising method to visualize the peripheral nerves. In this study, the application value of 3D DW-SSFP brachial plexus imaging in the diagnosis of brachial plexus injury (BPI) was investigated. 33 patients with BPI were prospectively examined using 3D DW-SSFP MR neurography (MRN) of brachial plexus. Results of 3D DW-SSFP MRN were compared with intraoperative findings and measurements of electromyogram (EMG) or somatosensory evoked potentials (SEP) for each injured nerve root. 3D DW-SSFP MRN of brachial plexus has enabled good visualization of the small components of the brachial plexus. The postganglionic section of the brachial plexus was clearly visible in 26 patients, while the preganglionic section of the brachial plexus was clearly visible in 22 patients. Pseudomeningoceles were commonly observed in 23 patients. Others finding of MRN of brachial plexus included spinal cord offset (in 16 patients) and spinal cord deformation (in 6 patients). As for the 3D DW-SSFP MRN diagnosis of preganglionic BPI, the sensitivity, the specificity and the accuracy were respectively 96.8%, 90.29%, and 94.18%. 3D DW-SSFP MRN of brachial plexus improve visualization of brachial plexus and benefit to determine the extent of injury.
Analyses of RNA-Seq and sRNA-Seq data reveal a complex network of anti-viral defense in TCV-infected Arabidopsis thaliana
Authors: Wu Chao , Li Xinyue , Guo Song , Wong Sek-Man 
Published: October 2016

AbstractIn order to identify specific plant anti-viral genes related to the miRNA regulatory pathway, RNA-Seq and sRNA-Seq were performed using Arabidopsis WT and dcl1-9 mutant line. A total of 5,204 DEGs were identified in TCV-infected WT plants. In contrast, only 595 DEGs were obtained in the infected dcl1-9 mutant plants. GO enrichment analysis of the shared DEGs and dcl1-9 unique DEGs showed that a wide range of biological processes were affected in the infected WT plants. In addition, miRNAs displayed different patterns between mock and infected WT plants. This is the first global view of dcl1-9 transcriptome which provides TCV responsive miRNAs data. In conclusion, our results indicated the significance of DCL1 and suggested that PPR genes may play an important role in plant anti-viral defense.
Being overweight in early adulthood is associated with increased mortality in middle age
Authors: Carslake David , Jeffreys Mona , Davey Smith George 
Published: October 2016

AbstractObservational analyses of the association between body mass index (BMI) and all-cause mortality often suggest that overweight is neutral or beneficial, but such analyses are potentially confounded by smoking or by reverse causation. The use of BMI measured in early adulthood offers one means of reducing the latter problem. We used a cohort who were first measured while 16–24 year old students at Glasgow University in 1948–1968 and subsequently re-measured in 2000–2003, offering a rare opportunity to compare BMI measured at different ages as a predictor of mortality. Analysis of the later BMI measurements suggested that overweight was beneficial to survival, while analysis of BMI measured in early adulthood suggested that overweight was harmful and that the optimum BMI lay towards the lower end of the recommended range of 18.5–25 kg m−2. We interpret the association with later BMI as being probably distorted by reverse causality, although it remains possible instead that the optimum BMI increases with age. Differences when analyses were restricted to healthy non-smokers also suggested some residual confounding by smoking. These results suggest that analyses of BMI recorded in middle or old age probably over-estimate the optimum BMI for survival and should be treated with caution.
Intrinsic and extrinsic pinning in NdFeAs(O,F): vortex trapping and lock-in by the layered structure
Authors: Tarantini C. , Iida K. , Hänisch J. , Kurth F. , Jaroszynski J. , Sumiya N. , Chihara M. , Hatano T. , Ikuta H. , Schmidt S. , Seidel P. , Holzapfel B. , Larbalestier D. C. 
Published: October 2016

AbstractFe-based superconductors (FBS) present a large variety of compounds whose properties are affected to different extents by their crystal structures. Amongst them, theREFeAs(O,F) (RE1111,REbeing a rare-earth element) is the family with the highest critical temperatureTcbut also with a large anisotropy and Josephson vortices as demonstrated in the flux-flow regime in Sm1111 (Tc ∼ 55 K). Here we focus on the pinning properties of the lower-TcNd1111 in the flux-creep regime. We demonstrate that forH//ccritical current densityJcat high temperatures is dominated by point-defect pinning centres, whereas at low temperatures surface pinning by planar defects parallel to thec-axis and vortex shearing prevail. When the field approaches theab-planes, two different regimes are observed at low temperatures as a consequence of the transition between 3D Abrikosov and 2D Josephson vortices: one is determined by the formation of a vortex-staircase structure and one by lock-in of vortices parallel to the layers. This is the first study on FBS showing this behaviour in the full temperature, field, and angular range and demonstrating that, despite the lowerTcand anisotropy of Nd1111 with respect to Sm1111, this compound is substantially affected by intrinsic pinning generating a strongab-peak inJc.
Risk Factors for Sporadic Pancreatic Neuroendocrine Tumors: A Case-Control Study
Authors: Ben Qiwen , Zhong Jie , Fei Jian , Chen Haitao , Yv Lifen , Tan Jihong , Yuan Yaozong 
Published: October 2016

AbstractThe current study examined risk factors for sporadic pancreatic neuroendocrine tumors (PNETs), including smoking, alcohol use, first-degree family history of any cancer (FHC), and diabetes in the Han Chinese ethnic group. In this clinic-based case-control analysis on 385 patients with sporadic PNETs and 614 age- and sex-matched controls, we interviewed subjects using a specific questionnaire on demographics and potential risk factors. An unconditional multivariable logistic regression analysis was used to estimate adjusted odds ratios (AORs). No significant differences were found between patients and controls in terms of demographic variables. Most of the patients with PNETs had well-differentiated PNETs (G1, 62.9%) and non-advanced European Neuroendocrine Tumor Society (ENETS) stage (stage I or II, 83.9%). Ever/heavy smoking, a history of diabetes and a first-degree FHC were independent risk factors for non-functional PNETs. Only heavy drinking was found to be an independent risk factor for functional PNETs (AOR = 1.87; 95% confidence interval [CI], 1.01–3.51). Ever/heavy smoking was also associated with advanced ENETS staging (stage III or IV) at the time of diagnosis. This study identified first-degree FHC, ever/heavy smoking, and diabetes as risk factors for non-functional PNETs, while heavy drinking as a risk factor for functional PNETs.
HASE: Framework for efficient high-dimensional association analyses
Authors: Roshchupkin G. V. , Adams H. H. H. , Vernooij M. W. , Hofman A. , Van Duijn C. M. , Ikram M. A. , Niessen W. J. 
Published: October 2016

AbstractHigh-throughput technology can now provide rich information on a person’s biological makeup and environmental surroundings. Important discoveries have been made by relating these data to various health outcomes in fields such as genomics, proteomics, and medical imaging. However, cross-investigations between several high-throughput technologies remain impractical due to demanding computational requirements (hundreds of years of computing resources) and unsuitability for collaborative settings (terabytes of data to share). Here we introduce the HASE framework that overcomes both of these issues. Our approach dramatically reduces computational time from years to only hours and also requires several gigabytes to be exchanged between collaborators. We implemented a novel meta-analytical method that yields identical power as pooled analyses without the need of sharing individual participant data. The efficiency of the framework is illustrated by associating 9 million genetic variants with 1.5 million brain imaging voxels in three cohorts (total N = 4,034) followed by meta-analysis, on a standard computational infrastructure. These experiments indicate that HASE facilitates high-dimensional association studies enabling large multicenter association studies for future discoveries.