bluuebunny/crossref_metadata_2025_split huggingface dataset:
An oligonucleotide synthesizer based on a microreactor chip and an inkjet printer
Authors: Li Hui , Huang Ye , Wei Zewen , Wang Wei , Yang Zhenjun , Liang Zicai , Li Zhihong 
Published: March 2019

AbstractSynthetic oligonucleotides (oligos) are important tools in the fields of molecular biology and genetic engineering. For applications requiring a large number of oligos with high concentration, it is critical to perform high throughput oligo synthesis and achieve high yield of each oligo. This study reports a microreactor chip for oligo synthesis. By incorporating silica beads in the microreactors, the surface area of the solid substrate for oligo synthesis increases significantly in each microreactor. These beads are fixed in the microreactors to withstand the flushing step in oligo synthesis. Compared to conventional synthesis methods, this design is able to avoid protocols to hold the beads and integrate more microreactors on a chip. An inkjet printer is utilized to deliver chemical reagents in the microreactors. To evaluate the feasibility of oligo synthesis using this proof-of-concept synthesizer, an oligo with six nucleotide units is successfully synthesized.
Enhancing entanglement detection of quantum optical frequency combs via stimulated emission
Authors: Arkhipov Ievgen I. , Yoon Tai Hyun , Miranowicz Adam 
Published: March 2019

AbstractWe investigate the performance of a certain nonclassicality identifier, expressed via integrated second-order intensity moments of optical fields, in revealing bipartite entanglement of quantum-optical frequency combs (QOFCs), which are generated in both spontaneous and stimulated parametric down-conversion processes. We show that, by utilizing that nonclassicality identifier, one can well identify the entanglement of the QOFC directly from the experimentally measured intensity moments without invoking any state reconstruction techniques or homodyne detection. Moreover, we demonstrate that the stimulated generation of the QOFC improves the entanglement detection of these fields with the nonclassicality identifier. Additionally, we show that the nonclassicality identifier can be expressed in a factorized form of detectors quantum efficiencies and the number of modes, if the QOFC consists of many copies of the same two-mode twin beam. As an example, we apply the nonclassicality identifier to two specific types of QOFC, where: (i) the QOFC consists of many independent two-mode twin beams with non-overlapped spatial frequency modes, and (ii) the QOFC contains entangled spatial frequency modes which are completely overlapped, i.e., each mode is entangled with all the remaining modes in the system. We show that, in both cases, the nonclassicality identifier can reveal bipartite entanglement of the QOFC including noise, and that it becomes even more sensitive for the stimulated processes.
Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome
Authors: Shin Seung Chul , Kim Hyun , Lee Jun Hyuck , Kim Han-Woo , Park Joonho , Choi Beom-Soon , Lee Sang-Choon , Kim Ji Hee , Lee Hyoungseok , Kim Sanghee 
Published: March 2019

AbstractParochlus steinenii is a winged midge from King George Island. It is cold-tolerant and endures the harsh Antarctic winter. Previously, we reported the genome of this midge, but the genome assembly with short reads had limited contig contiguity, which reduced the completeness of the genome assembly and the annotated gene sets. Recently, assembly contiguity has been increased using nanopore technology. A number of methods for enhancing the low base quality of the assembly have been reported, including long-read (e.g. Nanopolish) or short-read (e.g. Pilon) based methods. Based on these advances, we used nanopore technologies to upgrade the draft genome sequence of P. steinenii. The final assembled genome was 145,366,448 bases in length. The contig number decreased from 9,132 to 162, and the N50 contig size increased from 36,946 to 1,989,550 bases. The BUSCO completeness of the assembly increased from 87.8 to 98.7%. Improved assembly statistics helped predict more genes from the draft genome of P. steinenii. The completeness of the predicted gene model increased from 79.5 to 92.1%, but the numbers and types of the predicted repeats were similar to those observed in the short read assembly, with the exception of long interspersed nuclear elements. In the present study, we markedly improved the P. steinenii genome assembly statistics using nanopore sequencing, but found that genome polishing with high-quality reads was essential for improving genome annotation. The number of genes predicted and the lengths of the genes were greater than before, and nanopore technology readily improved genome information.
Targeting Modified Lipids during Routine Lipidomics Analysis using HILIC and C30 Reverse Phase Liquid Chromatography coupled to Mass Spectrometry
Authors: Pham Thu Huong , Zaeem Muhammad , Fillier Tiffany A. , Nadeem Muhammad , Vidal Natalia P. , Manful Charles , Cheema Sukhinder , Cheema Mumtaz , Thomas Raymond H. 
Published: March 2019

AbstractLipids are important biomolecules in all biological systems and serve numerous essential cellular functions. The global analysis of complex lipids is very challenging due to the extreme diversity in lipid structures. Variation in linkages and positions of fatty acyl chain(s) on the lipid backbone, functional group modification, occurrence of the molecular species as isomers or isobars are among some of the greatest challenges to resolve in lipidomics. In this work, we describe a routine analytical approach combining two liquid chromatography platforms: hydrophilic interaction (HILIC) and C30 reversed-phase chromatography (C30RP) coupled to high resolution mass spectrometry (HRMS) as complementary high throughput platforms to analyze complex lipid mixtures. Vascular plants (kale leaves and corn roots), rat brain and soil microbes were used as proxies to evaluate the efficiency of the enhanced approach to resolve traditional, as well as, modified lipids during routine lipidomics analysis. We report for the first time, the observation of a modified class of acylphosphatidylglycerol (acylPG) in corn roots by HILIC, and further resolution of the isomers using C30RP chromatography. We also used this approach to demonstrate the presence of high levels of N-monomethyl phosphatidylethanolamine (MMPE) in soil microbes, as well as to determine the regioisomers of lysophospholipids in kale leaves. Additionally, neutral lipids were demonstrated using C30RP chromatography in positive ion mode to resolve triacylglycerol isomers in rat brain. The work presented here demonstrates how the enhanced approach can more routinely permit novel biomarker discovery, or lipid metabolism in a wide range of biological samples.
The contribution of super typhoons to tropical cyclone activity in response to ENSO
Authors: Kang Nam-Young , Kim Dongjin , Elsner James B. 
Published: March 2019

AbstractWestern North Pacific tropical cyclone (TC) activity is known to have a significant response to El Niño and Southern Oscillation (ENSO). Among the TC intensity classifications, “super typhoon”, is widely used as a symbolic word for warning people about the potential for experiencing the most severe typhoon. This study quantifies the contribution of super typhoons to TC activity in response to ENSO, where the Southern Oscillation Index (SOI) is used to indicate the internal variation of ENSO. It is found that the number and the genesis location of non-super typhoons are little influenced by ENSO, and the changes are mostly by the addition of super typhoons. Historical levels of El Niño and La Niña span from −2σ to +2σ of the SOI. Over this range of SOI values, the mean response is 5.6 super typhoons (7.1 for El Niño and 1.5 for La Niña) which nearly matches the mean response overall of 6 storms (24.6 for El Niño and 18.6 for La Niña). The spatial distribution of TC genesis locations for different ENSO conditions does not completely explain these results.
Phenylpyrrole fungicides act on triosephosphate isomerase to induce methylglyoxal stress and alter hybrid histidine kinase activity
Authors: Brandhorst T. Tristan , Kean Iain R. L. , Lawry Stephanie M. , Wiesner Darin L. , Klein Bruce S. 
Published: March 2019

AbstractFludioxonil, a natural product of pyrrolnitrin, is a potent fungicide used on crops worldwide. Drug action requires the presence of a group III hybrid histidine kinase (HHK) and the high osmolarity glycerol (HOG) pathway. We have reported that the drug does not act directly on HHK, but triggers the conversion of the kinase to a phosphatase, which dephosphorylates Ypd1 to constitutively activate HOG signaling. Still, the direct drug target remains unknown and mode of action ill defined. Here, we heterologously expressed a group III HHK, dimorphism-regulating kinase 1 (Drk1) in Saccharomyces cerevisae to delineate fludioxonil’s target and action. We show that the drug interferes with triosephosphate isomerase (TPI) causing release of methylglyoxal (MG). MG activates the group III HHK and thus the HOG pathway. Drug action involved Drk1 cysteine 392, as a C392S substitution increased drug resistance in vivo. Drug sensitivity was reversed by dimedone treatment, indicating Drk1 responds in vivo to an aldehydic stress. Fludioxonil treatment triggered elevated cytosolic methylglyoxal. Likewise, methylglyoxal treatment of Drk1-expressing yeast phenocopied treatment with fludioxonil. Fludioxonil directly inhibited TPI and also caused it to release methylglyoxal in vitro. Thus, TPI is a drug target of the phenylpyrrole class of fungicides, inducing elevated MG which alters HHK activity, likely converting the kinase to a phosphatase that acts on Ypd1 to trigger HOG pathway activation and fungal cell death.
Temperature Chaos, Memory Effect, and Domain Fluctuations in the Spiral Antiferromagnet Dy
Authors: Kustov Sergey , Liubimova Iuliia , Corró Miguel , Torrens-Serra Joan , Wang Xiebin , Haines Charles R. S. , Salje Ekhard K. H. 
Published: March 2019

AbstractThe spiral antiferromagnetic phase of polycrystalline dysprosium between 140 K and the Néel temperature at 178 K and its domain wall (DW) dynamics were investigated using high-resolution ultrasonic spectroscopy. Two kinetic processes of quasi-static DW motion occur under non-isothermal and isothermal conditions. A “fast” process is proportional to the rate of the temperature change and results in a new category of anelastic phenomena: magnetic transient ultrasonic internal friction (IF). This IF, related to fast moving magnetic DWs, decays rapidly after interruptions of cooling/heating cycles. A second, “slow” kinetic process is seen as logarithmic IF relaxation under isothermal conditions. This second process is glass-like and results in memory and temperature chaos effects. Low-frequency thermal fluctuations of DWs, previously detected by X-ray photon correlation spectroscopy, are related to critical fluctuations with Brownian motion-like dynamics of DWs.
Measurement of lactate levels in postmortem brain, iPSCs, and animal models of schizophrenia
Authors: Sullivan Courtney R. , Mielnik Catharine A. , Funk Adam , O’Donovan Sinead M. , Bentea Eduard , Pletnikov Mikhail , Ramsey Amy J. , Wen Zhexing , Rowland Laura M. , McCullumsmith Robert E. 
Published: March 2019

AbstractConverging evidence suggests bioenergetic defects contribute to the pathophysiology of schizophrenia and may underlie cognitive dysfunction. The transport and metabolism of lactate energetically couples astrocytes and neurons and supports brain bioenergetics. We examined the concentration of lactate in postmortem brain (dorsolateral prefrontal cortex) in subjects with schizophrenia, in two animal models of schizophrenia, the GluN1 knockdown mouse model and mutant disrupted in schizophrenia 1 (DISC1) mouse model, as well as inducible pluripotent stem cells (iPSCs) from a schizophrenia subject with the DISC1 mutation. We found increased lactate in the dorsolateral prefrontal cortex (p = 0.043, n = 16/group) in schizophrenia, as well as in frontal cortical neurons differentiated from a subject with schizophrenia with the DISC1 mutation (p = 0.032). We also found a decrease in lactate in mice with induced expression of mutant human DISC1 specifically in astrocytes (p = 0.049). These results build upon the body of evidence supporting bioenergetic dysfunction in schizophrenia, and suggests changes in lactate are a key feature of this often devastating severe mental illness.
A Genome-Wide Analysis of the Penumbral Volume in Inbred Mice following Middle Cerebral Artery Occlusion
Authors: Rudy Robert F. , Charoenvimolphan Nareerat , Qian Baogang , Berndt Annerose , Friedlander Robert M. , Weiss Scott T. , Du Rose 
Published: March 2019

AbstractFollowing ischemic stroke, the penumbra, at-risk neural tissue surrounding the core infarct, survives for a variable period of time before progressing to infarction. We investigated genetic determinants of the size of penumbra in mice subjected to middle cerebral artery occlusion (MCAO) using a genome-wide approach. 449 male mice from 33 inbred strains underwent MCAO for 6 hours (215 mice) or 24 hours (234 mice). A genome-wide association study using genetic data from the Mouse HapMap project was performed to examine the effects of genetic variants on the penumbra ratio, defined as the ratio of the infarct volume after 6 hours to the infarct volume after 24 hours of MCAO. Efficient mixed model analysis was used to account for strain interrelatedness. Penumbra ratio differed significantly by strain (F = 2.7, P < 0.001) and was associated with 18 significant SNPs, including 6 protein coding genes. We have identified 6 candidate genes for penumbra ratio: Clint1, Nbea, Smtnl2, Rin3, Dclk1, and Slc24a4.
On the stress-strain alignment in premixed turbulent flames
Authors: Ahmed Umair , Chakraborty Nilanjan , Klein Markus 
Published: March 2019

AbstractThe interaction of large and small scale structures is fundamental to the energy cascade in turbulent flows. The correct representation of this interaction becomes important in the context of large eddy simulation (LES), where the response of small-scale structures to the resolved quantities, or large-scale structures, must be parametrised. This challenging task becomes more demanding when LES of premixed flames are considered, as heat release affects the interaction of turbulence and chemistry occurring at the unresolved scales. In this work, the influence of sub-grid scale (SGS) stresses on the kinetic energy budget of the resolved velocity field in turbulent premixed flames is investigated. In this spirit, the alignment between the SGS stresses and the resolved strain rate has been analysed by interrogating a direct numerical simulation (DNS) database of statistically planar premixed flames subjected to forced isotropic turbulence. It has been found that the alignment between the eigenvectors of the SGS stresses and the resolved strain rate changes across the flame brush and this change is dependent on the level of turbulence experienced by the flame. The influence of different turbulence intensities and different filter widths along with the implications of this misalignment on the SGS modelling are discussed in detail in the paper.
Genome-wide Analysis Reveals DNA Methylation Alterations in Obesity Associated with High Risk of Colorectal Cancer
Authors: Dong Lixin , Ma Li , Ma Gloria H. , Ren Hongmei 
Published: March 2019

AbstractObesity is a high risk factor for colorectal cancer (CRC). The contribution of underlying epigenetic mechanisms to CRC and the precise targets of epigenetic alterations during cancer development are largely unknown. Several types of epigenetic processes have been described, including DNA methylation, histone modification, and microRNA expression. To investigate the relationship between obesity and CRC, we studied both obese and CRC patients, focusing on genome-wide peripheral blood DNA methylation alterations. Our results show abnormal distributions of overlapping differentially methylated regions (DMRs) such as hypermethylated CpG islands, which may account for epigenetic instability driving cancer initiation in obesity patients. Furthermore, functional analysis suggests that altered DNA methylation of extracellular (e.g., O-glycan processing) and intracellular components contribute to activation of oncogenes (e.g. KRAS and SCL2A1) and suppression of tumor suppressors (e.g. ARHGEF4, EPHB2 and SOCS3), leading to increased oncogenic potency. Our study demonstrates how DNA methylation changes in obesity contribute to CRC development, providing direct evidence of an association between obesity and CRC. It also reveals the diagnostic potential of using DNA methylation as an early risk evaluation to detect patients with high risk for CRC.
The influence of a single hemodialysis procedure on human T lymphocytes
Authors: Lisowska Katarzyna A. , Pindel Małgorzata , Pietruczuk Krzysztof , Kuźmiuk-Glembin Izabella , Storoniak Hanna , Dębska-Ślizień Alicja , Witkowski Jacek M. 
Published: March 2019

AbstractAt the moment it is unknown to what extent the impaired function of T lymphocytes in ESRD patients depends on uremia, and to what extent on hemodialysis (HD) procedure. Therefore, the purpose of the study was to evaluate percentages of T lymphocyte subpopulations ex vivo, plasma concentrations of IL12p70, TNF, IL-10, IL-6, IL-1β, IL-8 cytokines and selected proliferation parameters of in vitro activated T lymphocytes in HD patients before and after single HD procedure using flow cytometry. We demonstrated that the percentage of CD8+ cells ex vivo was decreased while the CD4+/CD8+ ratio was increased after HD procedure. Also, there was significant decrease in the percentage of CD8+HLA-DR+, CD8+CD69+ and CD8+CD95+ cells after HD. At the same time, an increase in the percentage of CD4+CD95+ cells was observed after HD. From all analyzed cytokines, only the concentration of IL-8 was significantly decreased after HD procedure. A single HD session enhanced proliferation capacity of CD4+ cells but not CD8+ cells in vitro by increasing number of cell divisions and percentage of dividing cells. Our results show that a single hemodialysis can have immunomodulatory effect on HD patients and may contribute to the state of immune deficiency observed in patients with ESRD.
Risk factors associated with locoregional failure and estimation of survival after curative resection for patients with distal bile duct cancer
Authors: Im Jung Ho , Park Joon Seong , Yoon Dong Sup , Lee Dong Ki , Kim Jun Won , Lee Ik Jae 
Published: March 2019

AbstractOur aim was to identify the risk factors associated with locoregional recurrence in resected distal bile duct cancer (DBDC), and to determine the subgroup that may benefit from adjuvant radiotherapy. Between 2001 and 2013, we retrospectively analyzed 93 patients with DBDC who had undergone curative resection. Patients who received adjuvant radiotherapy were excluded. The 3-year locoregional failure-free survival (LRFFS) and overall survival (OS) rates for all patients were 50.7%, and 53.2%, respectively. On multivariate analysis, the preoperative carcinoembryonic antigen (CEA) level, resection margin, histologic grade, T stage, and N stage were significant prognostic factors for LRFFS. Locoregional recurrence was observed in more than 78% of the patients who underwent R1 resection and were node-positive, and the 3-year LRFFS rate was 19.3%. The 3-year LRFFS rate was 46.9% in the patients who underwent R0 resection and were node-negative with more than 2 risk factors (preoperative CEA level ≥ 5 ng/mL, poorly differentiated histologic grade, and T3 stage). On multivariate analysis for OS, patients with more than 2 risk factors showed a 7-fold higher risk of death, compared with patients with 1 or no risk factor. The important risk factors of locoregional failure in patients with DBDC who underwent resection were R1 resection and positive lymph nodes. Adjuvant radiotherapy should be considered for these patients to improve the oncologic outcomes. Patients undergoing selective R0 resection and those with node-negative status and multiple locoregional failure risk factors may benefit from adjuvant radiotherapy.
Genetic polymorphisms in MTR are associated with non-syndromic congenital heart disease from a family-based case-control study in the Chinese population
Authors: Deng Changfei , Deng Ying , Xie Liang , Yu Li , Liu Lijun , Liu Hanmin , Dai Li 
Published: March 2019

AbstractGenetic polymorphisms of folate pathway genes have been reported to be associated with congenital heart diseases (CHDs); however, the results remain conflicting. We conducted a family-based case-control study, which included160 CHD case-parent triads and 208 control-parent triads to explore the association of 18 genetic variants of seven folate metabolism-related genes with the risk of CHDs. The MTR C allele of rs1770449 (OR = 1.961, 95%CI: 1.379–2.788) and the MTR A allele of rs1050993 (OR = 1.994, 95%CI: 1.401–2.839) in infants were associated with an increased risk of CHDs. Over-transmission of SNPs rs1770449 and rs1050993 and haplotype CAA (rs1770449-rs1805087-rs1050993) in MTR were detected in total CHDs. The above mentioned associations of MTR with CHDs were also observed in septal defects and conotruncal heart defects subgroups. Without maternal periconceptional folate intake, the risk of CHDs among women carrying the rs1770449 “CT or CC” genotype or the rs1050993 “AG or AA” genotype in MTR was 3.262(95%CI: 1.656–6.429) or 3.263(95%CI: 1.656–6.429) times greater than the aOR in women carrying wild genotype, respectively. Our study suggests that MTR polymorphisms (rs1770449 and rs1050993) may be associated with the risk of CHDs and modify the relation between maternal folate intake and CHDs.
Crosssectional Assessment of Bone Mass Density in Adults with Hepatitis B Virus and Hepatitis C Virus Infection
Authors: Chen Yuan-Yuei , Fang Wen-Hui , Wang Chung-Ching , Kao Tung-Wei , Chang Yaw-Wen , Yang Hui-Fang , Wu Chen-Jung , Sun Yu-Shan , Chen Wei-Liang 
Published: March 2019

AbstractOsteoporosis is one of the major complications in chronic hepatitis B virus (HBV) and hepatitis C (HCV) infection. However, few studies had examined the relationship between hepatic viral infection with bone loss. Our aim was to investigate the association between hepatic viral infection with bone mineral density (BMD) in a cross-sectional study. Participants who attended the health examinations at the Tri-Service General Hospital (TSGH), Taiwan, were enrolled in the study. Diagnosis of viral hepatitis was confirmed by the serum viral markers of hepatitis B surface antigen (HBsAg) and anti-HCV, and BMD measurement was performed by the bone densitometry. Subjects were divided into four groups by the presence of viral markers. The association between hepatic viral infection and BMD was examined by a multivariate linear regression model. HBV infection was inversely associated with BMD after full adjusting withβvalues of −0.17 (95% CI: −0.29, −0.05) (p < 0.05). The relationship remained significant in males (β = −0.16, 95% CI = −0.31, −0.01) (p < 0.05). In subjects with body mass index less than 30 HBV infection was associated with reduced BMD (β = −0.16, 95% CI = −0.29, −0.02) (p < 0.05). However, HCV infection was only associated with an increase in BMD in patients with BMI less than 30 (β = 0.17, 95% CI = 0.21, 0.32) (p < 0.05). Chronic HBV infection was significantly associated with reduced BMD in males. The impact of viral hepatitis on bone health deserves further investigation for the potential pathophysiological mechanisms.