bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrophoresis of polar fluorescent tracers through the nerve sheath labels neuronal populations for anatomical and functional imaging
Authors: Isaacson Matthew D. , Hedwig Berthold 
Published: January 2017

AbstractThe delivery of tracers into populations of neurons is essential to visualize their anatomy and analyze their function. In some model systems genetically-targeted expression of fluorescent proteins is the method of choice; however, these genetic tools are not available for most organisms and alternative labeling methods are very limited. Here we describe a new method for neuronal labelling by electrophoretic dye delivery from a suction electrode directly through the neuronal sheath of nerves and ganglia in insects. Polar tracer molecules were delivered into the locust auditory nerve without destroying its function, simultaneously staining peripheral sensory structures and central axonal projections. Local neuron populations could be labelled directly through the surface of the brain, and in-vivo optical imaging of sound-evoked activity was achieved through the electrophoretic delivery of calcium indicators. The method provides a new tool for studying how stimuli are processed in peripheral and central sensory pathways and is a significant advance for the study of nervous systems in non-model organisms.
Increased Renal Clearance of Rocuronium Compensates for Chronic Loss of Bile Excretion, via upregulation of Oatp2
Authors: Wang Long , Zhou Mai-Tao , Chen Cai-Yang , Yin Wen , Wen Da-Xiang , Cheung Chi-Wai , Yang Li-Qun , Yu Wei-Feng 
Published: January 2017

AbstractRequirement for rocuronium upon surgery changes only minimally in patients with end-stage liver diseases. Our study consisted of both human and rat studies to explore the reason. The reduction rate of rocuronium infusion required to maintain neuromuscular blockade during the anhepatic phase (relative to paleohepatic phase) was examined in 16 children with congenital biliary atresia receiving orthotopic liver transplantation. Pharmacodynamics and pharmacokinetics of rocuronium were studied based on BDL rats. The role of increased Oatp2 and decrease Oatp1 expressions in renal compensation were explored. The reduction of rocuronium requirements significantly decreased in obstructively jaundiced children (24 ± 9 vs. 39 ± 11%). TOF50 in BDL rats was increased by functional removal of the kidneys but not the liver, and the percentage of rocuronium excretion through urine increased (20.3 ± 6.9 vs. 8.6 ± 1.8%), while that decreased through bile in 28d-BDL compared with control group. However, this enhanced renal secretion for rocuronium was eliminated by Oatp2 knock-down, rather than Oatp1 overexpression (28-d BDL vs. Oatp1-ShRNA or Oatp2-ShRNA, 20.3 ± 6.9 vs. 17.0 ± 6.6 or 9.3 ± 3.2%). Upon chronic/sub-chronic loss of bile excretion, rocuronium clearance via the kidneys is enhanced, by Oatp2 up-regulation.
White to beige conversion in PDE3B KO adipose tissue through activation of AMPK signaling and mitochondrial function
Authors: Chung Youn Wook , Ahmad Faiyaz , Tang Yan , Hockman Steven C. , Kee Hyun Jung , Berger Karin , Guirguis Emilia , Choi Young Hun , Schimel Dan M. , Aponte Angel M. , Park Sunhee , Degerman Eva , Manganiello Vincent C. 
Published: January 2017

AbstractUnderstanding mechanisms by which a population of beige adipocytes is increased in white adipose tissue (WAT) reflects a potential strategy in the fight against obesity and diabetes. Cyclic adenosine monophosphate (cAMP) is very important in the development of the beige phenotype and activation of its thermogenic program. To study effects of cyclic nucleotides on energy homeostatic mechanisms, mice were generated by targeted inactivation of cyclic nucleotide phosphodiesterase 3b (Pde3b) gene, which encodes PDE3B, an enzyme that catalyzes hydrolysis of cAMP and cGMP and is highly expressed in tissues that regulate energy homeostasis, including adipose tissue, liver, and pancreas. In epididymal white adipose tissue (eWAT) of PDE3B KO mice on a SvJ129 background, cAMP/protein kinase A (PKA) and AMP-activated protein kinase (AMPK) signaling pathways are activated, resulting in “browning” phenotype, with a smaller increases in body weight under high-fat diet, smaller fat deposits, increased β-oxidation of fatty acids (FAO) and oxygen consumption. Results reported here suggest that PDE3B and/or its downstream signaling partners might be important regulators of energy metabolism in adipose tissue, and potential therapeutic targets for treating obesity, diabetes and their associated metabolic disorders.
Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways
Authors: Kaushik Abhinav , Ali Shakir , Gupta Dinesh 
Published: January 2017

AbstractGene connection rewiring is an essential feature of gene network dynamics. Apart from its normal functional role, it may also lead to dysregulated functional states by disturbing pathway homeostasis. Very few computational tools measure rewiring within gene co-expression and its corresponding regulatory networks in order to identify and prioritize altered pathways which may or may not be differentially regulated. We have developed Altered Pathway Analyzer (APA), a microarray dataset analysis tool for identification and prioritization of altered pathways, including those which are differentially regulated by TFs, by quantifying rewired sub-network topology. Moreover, APA also helps in re-prioritization of APA shortlisted altered pathways enriched with context-specific genes. We performed APA analysis of simulated datasets and p53 status NCI-60 cell line microarray data to demonstrate potential of APA for identification of several case-specific altered pathways. APA analysis reveals several altered pathways not detected by other tools evaluated by us. APA analysis of unrelated prostate cancer datasets identifies sample-specific as well as conserved altered biological processes, mainly associated with lipid metabolism, cellular differentiation and proliferation. APA is designed as a cross platform tool which may be transparently customized to perform pathway analysis in different gene expression datasets. APA is freely available at http://bioinfo.icgeb.res.in/APA.
The short-term effects of air pollutants on respiratory disease mortality in Wuhan, China: comparison of time-series and case-crossover analyses
Authors: Ren Meng , Li Na , Wang Zhan , Liu Yisi , Chen Xi , Chu Yuanyuan , Li Xiangyu , Zhu Zhongmin , Tian Liqiao , Xiang Hao 
Published: January 2017

AbstractFew studies have compared different methods when exploring the short-term effects of air pollutants on respiratory disease mortality in Wuhan, China. This study assesses the association between air pollutants and respiratory disease mortality with both time-series and time-stratified–case-crossover designs. The generalized additive model (GAM) and the conditional logistic regression model were used to assess the short-term effects of air pollutants on respiratory disease mortality. Stratified analyses were performed by age, sex, and diseases. A 10 μg/m3 increment in SO2 level was associated with an increase in relative risk for all respiratory disease mortality of 2.4% and 1.9% in the case-crossover and time-series analyses in single pollutant models, respectively. Strong evidence of an association between NO2 and daily respiratory disease mortality among men or people older than 65 years was found in the case-crossover study. There was a positive association between air pollutants and respiratory disease mortality in Wuhan, China. Both time-series and case-crossover analyses consistently reveal the association between three air pollutants and respiratory disease mortality. The estimates of association between air pollution and respiratory disease mortality from the case–crossover analysis displayed greater variation than that from the time-series analysis.
Genome-wide DNA methylation profile in mungbean
Authors: Kang Yang Jae , Bae Ahra , Shim Sangrea , Lee Taeyoung , Lee Jayern , Satyawan Dani , Kim Moon Young , Lee Suk-Ha 
Published: January 2017

AbstractDNA methylation on cytosine residues is known to affect gene expression and is potentially responsible for the phenotypic variations among different crop cultivars. Here, we present the whole-genome DNA methylation profiles and assess the potential effects of single nucleotide polymorphisms (SNPs) for two mungbean cultivars, Sunhwanogdu (VC1973A) and Kyunggijaerae#5 (V2984). By measuring the DNA methylation levels in leaf tissue with the bisulfite sequencing (BSseq) approach, we show both the frequencies of the various types of DNA methylation and the distribution of weighted gene methylation levels. SNPs that cause nucleotide changes from/to CHH – where C is cytosine and H is any other nucleotide – were found to affect DNA methylation status in VC1973A and V2984. In order to better understand the correlation between gene expression and DNA methylation levels, we surveyed gene expression in leaf tissues of VC1973A and V2984 using RNAseq. Transcript expressions of paralogous genes were controlled by DNA methylation within the VC1973A genome. Moreover, genes that were differentially expressed between the two cultivars showed distinct DNA methylation patterns. Our mungbean genome-wide methylation profiles will be valuable resources for understanding the phenotypic variations between different cultivars, as well as for molecular breeding.
A Conditional Knockout Mouse Model Reveals a Critical Role of PKD1 in Osteoblast Differentiation and Bone Development
Authors: Li Shao , Xu Wanfu , Xing Zhe , Qian Jiabi , Chen Liping , Gu Ruonan , Guo Wenjing , Lai Xiaoju , Zhao Wanlu , Li Songyu , Wang Yaodong , Wang Q. Jane , Deng Fan 
Published: January 2017

AbstractThe protein kinase D family of serine/threonine kinases, particularly PKD1, has been implicated in the regulation of a complex array of fundamental biological processes. However, its function and mechanism underlying PKD1-mediated the bone development and osteoblast differentiation are not fully understood. Here we demonstrate that loss of PKD1 function led to impaired bone development and osteoblast differentiation through STAT3 and p38 MAPK signaling using in vitro and in vivo bone-specific conditional PKD1-knockout (PKD1-KO) mice models. These mice developed markedly craniofacial dysplasia, scapula dysplasia, long bone length shortage and body weight decrease compared with wild-type littermates. Moreover, deletion of PKD1 in vivo reduced trabecular development and activity of osteoblast development, confirmed by Micro-CT and histological staining as well as expression of osteoblastic marker (OPN, Runx2 and OSX). Mechanistically, loss of PKD1 mediated the downregulation of osteoblast markers and impaired osteoblast differentiation through STAT3 and p38 MAPK signaling pathways. Taken together, these results demonstrated that PKD1 contributes to the osteoblast differentiation and bone development via elevation of osteoblast markers through activation of STAT3 and p38 MAPK signaling pathways.
Common risk variants for colorectal cancer: an evaluation of associations with age at cancer onset
Authors: Song Nan , Shin Aesun , Park Ji Won , Kim Jeongseon , Oh Jae Hwan 
Published: January 2017

AbstractCommon genetic risk variants for colorectal cancer (CRC) have been identified at approximately 40 loci by genome-wide association studies (GWAS). We investigated the association of these risk variants by age at onset of CRC using case-only and case-control analysis. A total of 1,962 CRC cases and 2,668 controls from two independent case-control studies conducted by Korea’s National Cancer Center were included in this study. We genotyped 33 GWAS-identified single-nucleotide polymorphisms (SNPs) associated with CRC risk. The risk allele in SNP rs704017, located at 10q22.3 in the ZMIZ1-AS1 gene, was consistently less frequent among CRC patients aged <50 years than among CRC patients aged ≥50 years in the case-only analysis (odds ratio (OR) = 0.78, 95% confidence interval (CI) = 0.66–0.92, P = 2.7 × 10−3, in an additive model), although this did not surpass the threshold for multiple testing. The direction of associations between rs704017 and CRC risk differed by age group in the combined case-control analysis (<50 years: OR = 0.77, 95% CI = 0.60–0.98, P = 0.03 and ≥50 years: OR = 1.13, 95% CI = 0.98–1.29, P = 0.09, in a dominant model); the p-values for heterogeneity (Pheterogeneity = 7.5 × 10−3) and for interaction were statistically significant (Pinteraction = 7.8 × 10−3, in the dominant model). Our results suggest that the CRC susceptibility SNP rs704017 has a hereditary effect on onset age of CRC.
Impact and Origin of Interface States in MOS Capacitor with Monolayer MoS2 and HfO2 High-k Dielectric
Authors: Xia Pengkun , Feng Xuewei , Ng Rui Jie , Wang Shijie , Chi Dongzhi , Li Cequn , He Zhubing , Liu Xinke , Ang Kah-Wee 
Published: January 2017

AbstractTwo-dimensional layered semiconductors such as molybdenum disulfide (MoS2) at the quantum limit are promising material for nanoelectronics and optoelectronics applications. Understanding the interface properties between the atomically thin MoS2 channel and gate dielectric is fundamentally important for enhancing the carrier transport properties. Here, we investigate the frequency dispersion mechanism in a metal-oxide-semiconductor capacitor (MOSCAP) with a monolayer MoS2 and an ultra-thin HfO2 high-k gate dielectric. We show that the existence of sulfur vacancies at the MoS2-HfO2 interface is responsible for the generation of interface states with a density (Dit) reaching ~7.03 × 1011 cm−2 eV−1. This is evidenced by a deficit S:Mo ratio of ~1.96 using X-ray photoelectron spectroscopy (XPS) analysis, which deviates from its ideal stoichiometric value. First-principles calculations within the density-functional theory framework further confirms the presence of trap states due to sulfur deficiency, which exist within the MoS2 bandgap. This corroborates to a voltage-dependent frequency dispersion of ~11.5% at weak accumulation which decreases monotonically to ~9.0% at strong accumulation as the Fermi level moves away from the mid-gap trap states. Further reduction in Dit could be achieved by thermally diffusing S atoms to the MoS2-HfO2 interface to annihilate the vacancies. This work provides an insight into the interface properties for enabling the development of MoS2 devices with carrier transport enhancement.
Diabetes mellitus and the risk of total knee replacement among Chinese in Singapore, the Singapore Chinese Health Study
Authors: Leung Ying-Ying , Allen John Carson , Ang Li-Wei , Yuan Jian-Min , Koh Woon-Puay 
Published: January 2017

AbstractAssociation between diabetes mellitus (diabetes) and risk of knee osteoarthritis (KOA) is confounded by high body mass index (BMI), a strong risk factor for both conditions. We evaluated the association between diabetes and incidence of total knee replacement (TKR) due to severe KOA in the Singapore Chinese Health Study, a prospective cohort of 63,257 Chinese men and women, aged 45–74 years at recruitment in 1993–1998, and re-interviewed in 1999–2004. Height, weight, lifestyle factors and history of diabetes were obtained through in-person interviews at recruitment and re-interview. Incident cases of TKR were identified via record linkage with nationwide hospital discharge database. Subjects with/without prevalent diabetes had comparable BMI (24.0 kg/m2 versus 23.0 kg/m2). After an average of 14-years, 1,973 subjects had TKR attributable to KOA. Compared to subjects without diabetes, hazard ratio (HR) of TKR for subjects with diabetes was 0.63 [95% confidence interval (CI), 0.52–0.75] after controlling for BMI and other risk factors. An inverse association was also observed between incident diabetes at re-interview and subsequent risk of TKR (HR = 0.74; 95% CI = 0.58–0.94). The inverse diabetes-TKR risk association was similar by gender and across three categories of BMI. Our study does not support diabetes as a risk factor of KOA.
Population genomic insights into variation and evolution of Xanthomonas oryzae pv. oryzae
Authors: Midha Samriti , Bansal Kanika , Kumar Sanjeet , Girija Anil Madhusoodana , Mishra Deo , Brahma Kranthi , Laha Gouri Sankar , Sundaram Raman Meenakshi , Sonti Ramesh V. , Patil Prabhu B. 
Published: January 2017

AbstractXanthomonas oryzae pv. oryzae ( Xoo) is a serious pathogen of rice causing bacterial leaf blight disease. Resistant varieties and breeding programs are being hampered by the emergence of highly virulent strains. Herein we report population based whole genome sequencing and analysis of 100 Xoo strains from India. Phylogenomic analysis revealed the clustering of Xoo strains from India along with other Asian strains, distinct from African and US Xo strains. The Indian Xoo population consists of a major clonal lineage and four minor but highly diverse lineages. Interestingly, the variant alleles, gene clusters and highly pathogenic strains are primarily restricted to minor lineages L-II to L-V and in particularly to lineage L-III. We could also find the association of an expanded CRISPR cassette and a highly variant LPS gene cluster with the dominant lineage. Molecular dating revealed that the major lineage, L-I is youngest and of recent origin compared to remaining minor lineages that seems to have originated much earlier in the past. Further, we were also able to identify core effector genes that may be helpful in efforts towards building durable resistance against this pathogen.
De novo AML exhibits greater microenvironment dysregulation compared to AML with myelodysplasia-related changes
Authors: Lopes Matheus Rodrigues , Pereira João Kleber Novais , de Melo Campos Paula , Machado-Neto João Agostinho , Traina Fabiola , Saad Sara T. Olalla , Favaro Patricia 
Published: January 2017

AbstractThe interaction between the bone marrow microenvironment and malignant hematopoietic cells can result in the protection of leukemia cells from chemotherapy in both myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). We, herein, characterized the changes in cytokine expression and the function of mesenchymal stromal cells (MSC) in patients with MDS, AML with myelodysplasia-related changes (MRC), a well-recognized clinical subtype of secondary AML, andde novoAML. We observed a significant inhibitory effect of MDS-MSC on T lymphocyte proliferation and no significant differences in any of the cytokines tested. AML-MSC inhibited T-cell proliferation only at a very low MSC/T cell ratio. When compared to the control, AML-MRCderived MSC presented a significant increase inIL6expression, whereasde novoAML MSC presented a significant increase in the expression levels ofVEGFA, CXCL12, RPGE2, IDO, IL1β, IL6andIL32, followed by a decrease inIL10expression. Furthermore, data indicate that IL-32 regulates stromal cell proliferation, has a chemotactic potential and participates in stromal cell crosstalk with leukemia cells, which could result in chemoresistance. Our results suggest that the differences between AML-MRC andde novoAML also extend into the leukemic stem cell niche and that IL-32 can participate in the regulation of the bone marrow cytokine milieu.
Effects of individual micronutrients on blood pressure in patients with type 2 diabetes: a systematic review and meta-analysis of randomized clinical trials
Authors: de Paula Tatiana P. , Kramer Caroline K. , Viana Luciana V. , Azevedo Mirela J. 
Published: January 2017

AbstractTo investigate the effects of micronutrients on blood pressure (BP) in patients with type 2 diabetes through a systematic review and meta-analysis, randomized clinical trials (RCTs) of the effects of individual micronutrients on BP in patients with type 2 diabetes were searched in the Medline, Embase, Cochrane, and Clinical Trials.gov databases through April 2016. From the 28,164 studies, 11 RCTs (13 interventions, 723 patients, 54% males) with 3 to 52 weeks of follow-up were classified according to the type of micronutrient intervention: sodium (n = 1), vitamin C (n = 2), vitamin D (n = 7), and magnesium (n = 1). The available data enabled us to perform meta-analyses of vitamins C and D. Vitamin C reduced diastolic BP [WMD −2.88 mmHg (95%CI −5.31, −0.46; P = 0.020)] but not systolic BP [WMD −3.93 mmHg (95%CI −14.78, 6.92; P = 0.478)]. Vitamin D caused a reduction of 4.56 mmHg (WMD; 95%CI −7.65, −1.47; P = 0.004) for systolic BP and 2.44 mm Hg (WMD; 95%CI −3.49, −1.39; P < 0.001) for diastolic BP. In conclusion, vitamin D and possibly vitamin C have beneficial effects on BP in patients with type 2 diabetes. These interventions might represent a novel approach to the treatment of hypertension in these patients.
Stress barriers controlling lateral migration of magma revealed by seismic tomography
Authors: Martí J. , Villaseñor A. , Geyer A. , López C. , Tryggvason A. 
Published: January 2017

AbstractUnderstanding how monogenetic volcanic systems work requires full comprehension of the local and regional stresses that govern magma migration inside them and why/how they seem to change from one eruption to another. During the 2011–2012 El Hierro eruption (Canary Islands) the characteristics of unrest, including a continuous change in the location of seismicity, made the location of the future vent unpredictable, so short term hazard assessment was highly imprecise. A 3D P-wave velocity model is obtained using arrival times of the earthquakes occurred during that pre-eruptive unrest and several latter post-eruptive seismic crises not related to further eruptions. This model reveals the rheological and structural complexity of the interior of El Hierro volcanic island. It shows a number of stress barriers corresponding to regional tectonic structures and blocked pathways from previous eruptions, which controlled ascent and lateral migration of magma and, together with the existence of N-S regional compression, reduced its options to find a suitable path to reach the surface and erupt.
Tip-Enhanced Raman Scattering Imaging of Two-Dimensional Tungsten Disulfide with Optimized Tip Fabrication Process
Authors: Lee Chanwoo , Kim Sung Tae , Jeong Byeong Geun , Yun Seok Joon , Song Young Jae , Lee Young Hee , Park Doo Jae , Jeong Mun Seok 
Published: January 2017

AbstractWe successfully achieve the tip-enhanced nano Raman scattering images of a tungsten disulfide monolayer with optimizing a fabrication method of gold nanotip by controlling the concentration of etchant in an electrochemical etching process. By applying a square-wave voltage supplied from an arbitrary waveform generator to a gold wire, which is immersed in a hydrochloric acid solution diluted with ethanol at various ratios, we find that both the conical angle and radius of curvature of the tip apex can be varied by changing the ratio of hydrochloric acid and ethanol. We also suggest a model to explain the origin of these variations in the tip shape. From the systematic study, we find an optimal condition for achieving the yield of ~60% with the radius of ~34 nm and the cone angle of ~35°. Using representative tips fabricated under the optimal etching condition, we demonstrate the tip-enhanced Raman scattering experiment of tungsten disulfide monolayer grown by a chemical vapor deposition method with a spatial resolution of ~40 nm and a Raman enhancement factor of ~4,760.
Low pump threshold CVD graphene based passively harmonic mode‐locked fibre laser
Authors: Chow Kin Kee 
Published: January 2017

A low pump threshold passively harmonic mode‐locked fibre laser is demonstrated. The key component is a chemical vapour deposition grown graphene saturable absorber to enable higher order harmonic mode‐locking (HML) of the fibre laser with good output noise characteristics. With a relatively low pump power of 100 mW, the fibre laser generates ∼1 ps soliton pulses at the 21st order of HML with 40 dB of super‐mode noise suppression.