bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential expression of genes in the alate and apterous morphs of the brown citrus aphid, Toxoptera citricida
Authors: Shang Feng , Ding Bi-Yue , Xiong Ying , Dou Wei , Wei Dong , Jiang Hong-Bo , Wei Dan-Dan , Wang Jin-Jun 
Published: August 2016

AbstractWinged and wingless morphs in insects represent a trade-off between dispersal ability and reproduction. We studied key genes associated with apterous and alate morphs in Toxoptera citricida (Kirkaldy) using RNAseq, digital gene expression (DGE) profiling and RNA interference. The de novo assembly of the transcriptome was obtained through Illumina short-read sequencing technology. A total of 44,199 unigenes were generated and 27,640 were annotated. The transcriptomic differences between alate and apterous adults indicated that 279 unigenes were highly expressed in alate adults, whereas 5,470 were expressed at low levels. Expression patterns of the top 10 highly expressed genes in alate adults agreed with wing bud development trends. Silencing of the lipid synthesis and degradation gene (3-ketoacyl-CoA thiolase, mitochondrial-like) and glycogen genes (Phosphoenolpyruvate carboxykinase [GTP]-like and Glycogen phosphorylase-like isoform 2) resulted in underdeveloped wings. This suggests that both lipid and glycogen metabolism provide energy for aphid wing development. The large number of sequences and expression data produced from the transcriptome and DGE sequencing, respectively, increases our understanding of wing development mechanisms.
Chronic Rhinosinusitis Associated with Erectile Dysfunction: A Population-Based Study
Authors: Tai Shu-Yu , Wang Ling-Feng , Tai Chih-Feng , Huang Yu-Ting , Chien Chen-Yu 
Published: August 2016

AbstractFew studies have investigated the relationship between chronic rhinosinusitis (CRS) and erectile dysfunction (ED). This case-control study aimed to investigate the association between CRS and the risk of ED in a large national sample. Tapping Taiwan’s National Health Insurance Research Database, we identified people 30 years or older with a new primary diagnosis of CRS between 1996 and 2007. The cases were compared with sex- and age-matched controls. We identified 14 039 cases and recruited 140 387 matched controls. Both groups were followed up in the same database until the end of 2007 for instances of ED. Of those with CRS, 294 (2.1%) developed ED during a mean (SD) follow-up of 3.20 (2.33) years, while 1 661 (1.2%) of the matched controls developed ED, mean follow up 2.97 (2.39) years. Cox regression analyses were performed adjusting for sex, age, insurance premium, residence, hypertension, hyperlipidemia, diabetes, obesity, coronary heart disease, chronic kidney disease, chronic obstructive pulmonary disease, asthma, allergic rhinitis, arrhythmia, ischemic stroke, intracerebral hemorrhage, and medications. CRS was revealed to be an independent predictor of ED in the fully adjusted model (HR = 1.51; 95% CI = 1.33–1.73; P < 0.0001).
Individual dispersal decisions affect fitness via maternal rank effects in male rhesus macaques
Authors: Weiß Brigitte M. , Kulik Lars , Ruiz-Lambides Angelina V. , Widdig Anja 
Published: August 2016

AbstractNatal dispersal may have considerable social, ecological and evolutionary consequences. While species-specific dispersal strategies have received much attention, individual variation in dispersal decisions and its fitness consequences remain poorly understood. We investigated causes and consequences of natal dispersal age in rhesus macaques (Macaca mulatta), a species with male dispersal. Using long-term demographic and genetic data from a semi-free ranging population on Cayo Santiago, Puerto Rico, we analysed how the social environment such as maternal family, group and population characteristics affected the age at which males leave their natal group. While natal dispersal age was unrelated to most measures of group or population structure, our study confirmed earlier findings that sons of high-ranking mothers dispersed later than sons of low-ranking ones. Natal dispersal age did not affect males’ subsequent survival, but males dispersing later were more likely to reproduce. Late dispersers were likely to start reproducing while still residing in their natal group, frequently produced extra-group offspring before natal dispersal and subsequently dispersed to the group in which they had fathered offspring more likely than expected. Hence, the timing of natal dispersal was affected by maternal rank and influenced male reproduction, which, in turn affected which group males dispersed to.
Effect of BI-1 on insulin resistance through regulation of CYP2E1
Authors: Lee Geum-Hwa , Oh Kyoung-Jin , Kim Hyung-Ryong , Han Hye-Sook , Lee Hwa-Young , Park Keun-Gyu , Nam Ki-Hoan , Koo Seung-Hoi , Chae Han-Jung 
Published: August 2016

AbstractDiet-induced obesity is a major contributing factor to the progression of hepatic insulin resistance. Increased free fatty acids in liver enhances endoplasmic reticulum (ER) stress and production of reactive oxygen species (ROS), both are directly responsible for dysregulation of hepatic insulin signaling. BI-1, a recently studied ER stress regulator, was examined to investigate its association with ER stress and ROS in insulin resistance models. To induce obesity and insulin resistance, BI-1 wild type and BI-1 knock-out mice were fed a high-fat diet for 8 weeks. The BI-1 knock-out mice had hyperglycemia, was associated with impaired glucose and insulin tolerance under high-fat diet conditions. Increased activity of NADPH-dependent CYP reductase-associated cytochrome p450 2E1 (CYP2E1) and exacerbation of ER stress in the livers of BI-1 knock-out mice was also observed. Conversely, stable expression of BI-1 in HepG2 hepatocytes was shown to reduce palmitate-induced ER stress and CYP2E1-dependent ROS production, resulting in the preservation of intact insulin signaling. Stable expression of CYP2E1 led to increased ROS production and dysregulation of insulin signaling in hepatic cells, mimicking palmitate-mediated hepatic insulin resistance. We propose that BI-1 protects against obesity-induced hepatic insulin resistance by regulating CYP2E1 activity and ROS production.
Homogeneity and variation of donor doping in Verneuil-grown SrTiO3:Nb single crystals
Authors: Rodenbücher C. , Luysberg M. , Schwedt A. , Havel V. , Gunkel F. , Mayer J. , Waser R. 
Published: August 2016

AbstractThe homogeneity of Verneuil-grown SrTiO3:Nb crystals was investigated. Due to the fast crystal growth process, inhomogeneities in the donor dopant distribution and variation in the dislocation density are expected to occur. In fact, for some crystals optical studies show variations in the density of Ti3+states on the microscale and a cluster-like surface conductivity was reported in tip-induced resistive switching studies. However, our investigations by TEM, EDX mapping and 3D atom probe reveal that the Nb donors are distributed in a statistically random manner, indicating that there is clearly no inhomogeneity on the macro-, micro- and nanoscale in high quality Verneuil-grown crystals. In consequence, the electronic transport in the bulk of donor-doped crystals is homogeneous and it is not significantly channelled by extended defects such as dislocations which justifies using this material, for example, as electronically conducting substrate for epitaxial oxide film growth.
Intron retention-dependent gene regulation in Cryptococcus neoformans
Authors: Gonzalez-Hilarion Sara , Paulet Damien , Lee Kyung-Tae , Hon Chung-Chau , Lechat Pierre , Mogensen Estelle , Moyrand Frédérique , Proux Caroline , Barboux Rony , Bussotti Giovanni , Hwang Jungwook , Coppée Jean-Yves , Bahn Yong-Sun , Janbon Guilhem 
Published: August 2016

AbstractThe biological impact of alternative splicing is poorly understood in fungi, although recent studies have shown that these microorganisms are usually intron-rich. In this study, we re-annotated the genome of C. neoformans var. neoformans using RNA-Seq data. Comparison with C. neoformans var. grubii revealed that more than 99% of ORF-introns are in the same exact position in the two varieties whereas UTR-introns are much less evolutionary conserved. We also confirmed that alternative splicing is very common in C. neoformans, affecting nearly all expressed genes. We also observed specific regulation of alternative splicing by environmental cues in this yeast. However, alternative splicing does not appear to be an efficient method to diversify the C. neoformans proteome. Instead, our data suggest the existence of an intron retention-dependent mechanism of gene expression regulation that is not dependent on NMD. This regulatory process represents an additional layer of gene expression regulation in fungi and provides a mechanism to tune gene expression levels in response to any environmental modification.
Acetylated α-Tubulin Regulated by N-Acetyl-Seryl-Aspartyl-Lysyl-Proline(Ac-SDKP) Exerts the Anti-fibrotic Effect in Rat Lung Fibrosis Induced by Silica
Authors: Xiaojun Wang , Yan Liu , Hong Xu , Xianghong Zhang , Shifeng Li , Dingjie Xu , Xuemin Gao , Lijuan Zhang , Bonan Zhang , Zhongqiu Wei , Ruimin Wang , Brann Darrell , Fang Yang 
Published: August 2016

AbstractSilicosis is the most serious occupational disease in China. The objective of this study was to screen various proteins related to mechanisms of the pathogenesis of silicosis underlying the anti-fibrotic effect of N-acetyl-seryl-aspartyl-lysyl-proline (Ac-SDKP) using proteomic profile analysis. We also aimed to explore a potential mechanism of acetylated α-tubulin (α-Ac-Tub) regulation by Ac-SDKP. Two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) were used to assess the different protein expression profiles between control and silicosis rats treated with or without Ac-SDKP. Twenty-nine proteins were identified to be potentially involved in the progression of silicosis and the anti-fibrotic effect of Ac-SDKP. Our current study finds that 1) the lost expression of Ac-Tub-α may be a new mechanism in rat silicosis; 2) treatment of silicotic rats with N-acetyl-Seryl-Aspartyl-Lysyl-Proline (Ac-SDKP) inhibits myofibroblast differentiation and collagen deposition accompanied by stabilizing the expression of α-Ac-Tub in vivo and in vitro, which is related with deacetylase family member 6 (HDAC6) and α-tubulin acetyl transferase (α-TAT1). Our data suggest that α-Ac-Tub regulation by Ac-SDKP may potentially be a new anti-fibrosis mechanism.
Path (un)predictability of two interacting cracks in polycarbonate sheets using Digital Image Correlation
Authors: Koivisto J. , Dalbe M.-J. , Alava M. J. , Santucci S. 
Published: August 2016

AbstractCrack propagation is tracked here with Digital Image Correlation analysis in the test case of two cracks propagating in opposite directions in polycarbonate, a material with high ductility and a large Fracture Process Zone (FPZ). Depending on the initial distances between the two crack tips, one may observe different complex crack paths with in particular a regime where the two cracks repel each other prior to being attracted. We show by strain field analysis how this can be understood according to the principle of local symmetry: the propagation is to the direction where the local shear - mode KII in fracture mechanics language - is zero. Thus the interactions exhibited by the cracks arise from symmetry, from the initial geometry, and from the material properties which induce the FPZ. This complexity makes any long-range prediction of the path(s) impossible.
Observation of the Chiral and Achiral Hexatic Phases of Self-assembled Micellar polymers
Authors: Pal Antara , Kamal Md. Arif , Raghunathan V. A. 
Published: August 2016

AbstractWe report the discovery of a thermodynamically stable line hexatic (N + 6) phase in a three-dimensional (3D) system made up of self-assembledpolymer-likemicelles of amphiphilic molecules. The experimentally observed phase transition sequencenematic (N) "Equation missing" N + 6 "Equation missing" two-dimensional hexagonal (2D-H) is in good agreement with the theoretical predictions. Further, the present study also brings to light the effect of chirality on the N + 6 phase. In the chiral N + 6 phase the bond-orientational order within each “polymer” bundle is found to be twisted about an axis parallel to the average polymer direction. This structure is consistent with the theoretically envisaged Moiré state, thereby providing the first experimental demonstration of the Moiré structure. In addition to confirming the predictions of fundamental theories of two-dimensional melting, these results are relevant in a variety of situations in chemistry, physics and biology, where parallel packing of polymer-like objects are encountered.
Triclosan Resistome from Metagenome Reveals Diverse Enoyl Acyl Carrier Protein Reductases and Selective Enrichment of Triclosan Resistance Genes
Authors: Khan Raees , Kong Hyun Gi , Jung Yong-Hoon , Choi Jinhee , Baek Kwang-Yeol , Hwang Eul Chul , Lee Seon-Woo 
Published: August 2016

AbstractTriclosan (TCS) is a widely used antimicrobial agent and TCS resistance is considered to have evolved in diverse organisms with extensive use of TCS, but distribution of TCS resistance has not been well characterized. Functional screening of the soil metagenome in this study has revealed that a variety of target enoyl acyl carrier protein reductases (ENR) homologues are responsible for the majority of TCS resistance. Diverse ENRs similar to 7-α-hydroxysteroid dehydrogenase (7-α-HSDH), FabG, or the unusual YX7K-type ENR conferred extreme tolerance to TCS. The TCS-refractory 7-α HSDH-like ENR and the TCS-resistant YX7K-type ENR seem to be prevalent in human pathogenic bacteria, suggesting that a selective enrichment occurred in pathogenic bacteria in soil. Additionally, resistance to multiple antibiotics was found to be mediated by antibiotic resistance genes that co-localize with TCS resistance determinants. Further comparative analysis of ENRs from 13 different environments has revealed a huge diversity of both prototypic and metagenomic TCS-resistant ENRs, in addition to a selective enrichment of TCS-resistant specific ENRs in presumably TCS-contaminated environments with reduced ENR diversity. Our results suggest that long-term extensive use of TCS can lead to the selective emergence of TCS-resistant bacterial pathogens, possibly with additional resistance to multiple antibiotics, in natural environments.
A measure of the concentration of rare events
Authors: Prieto Curiel Rafael , Bishop Steven 
Published: August 2016

AbstractWe introduce here an index, which we call the Rare Event Concentration Coefficient (RECC), that is a measure of the dispersion/concentration of events which have a low frequency but tend to have a high level of concentration, such as the number of crimes suffered by a person. The Rare Event Concentration Coefficient is a metric based on a statistical mixture model, with a value closer to zero meaning that events are homogeneously distributed, and a value closer to one meaning that the events have a higher degree of concentration. This measure may be used to compare the concentration of events over different time periods and over different regions. Other traditional approaches for the dispersion/concentration of a variable tend to be blind to structural changes in the pattern of occurrence of rare events. The RECC overcomes this issue and we show here two simple applications, first by using the number of burglaries suffered in Netherlands and then by using the number of volcanic eruptions in the world.
N-acetylcysteine attenuates lipopolysaccharide-induced impairment in lamination of Ctip2-and Tbr1- expressing cortical neurons in the developing rat fetal brain
Authors: Chao Ming-Wei , Chen Chie-Pein , Yang Yu-Hsiu , Chuang Yu-Chen , Chu Tzu-Yun , Tseng Chia-Yi 
Published: August 2016

AbstractOxidative stress and inflammatory insults are the major instigating events of bacterial intrauterine infection that lead to fetal brain injury. The purpose of this study is to investigate the remedial effects of N-acetyl-cysteine (NAC) for inflammation-caused deficits in brain development. We found that lipopolysaccharide (LPS) induced reactive oxygen species (ROS) production by RAW264.7 cells. Macrophage-conditioned medium caused noticeable cortical cell damage, specifically in cortical neurons. LPS at 25 μg/kg caused more than 75% fetal loss in rats. An increase in fetal cortical thickness was noted in the LPS-treated group. In the enlarged fetal cortex, laminar positioning of the early born cortical cells expressing Tbr1 and Ctip2 was disrupted, with a scattered distribution. The effect was similar, but minor, in later born Satb2-expressing cortical cells. NAC protected against LPS-induced neuron toxicity in vitro and counteracted pregnancy loss and alterations in thickness and lamination of the neocortex in vivo. Fetal loss and abnormal fetal brain development were due to LPS-induced ROS production. NAC is an effective protective agent against LPS-induced damage. This finding highlights the key therapeutic impact of NAC in LPS-caused abnormal neuronal laminar distribution during brain development.
Fluorometric Measurement of Individual Stomata Activity and Transpiration via a “Brush-on”, Water-Responsive Polymer
Authors: Seo Minjeong , Park Dong-Hoon , Lee Chan Woo , Jaworski Justyn , Kim Jong-Man 
Published: August 2016

AbstractMuch of atmospheric water originates from transpiration, the process by which plants release H2O from pores, known as stomata, that simultaneously intake CO2 for photosynthesis. Controlling stomatal aperture can regulate the extent of water transport in response to dynamic environmental factors including osmotic stress, temperature, light, and wind. While larger leaf regions are often examined, the extent of water vapor release from individual stomata remains unexplored. Using a “brush-on” sensing material, we can now assess transpiration using a water-responsive, polydiacetylene-based coating on the leaves surfaces. By eliciting a fluorometric signal to passing water vapor, we obtained information regarding the activity of individual stomata. In this demonstration, our results prove that this coating can identify the proportion of active stomata and the extent of transpirational diffusion of water in response to different conditions.
Large-Scale Discovery of Disease-Disease and Disease-Gene Associations
Authors: Gligorijevic Djordje , Stojanovic Jelena , Djuric Nemanja , Radosavljevic Vladan , Grbovic Mihajlo , Kulathinal Rob J. , Obradovic Zoran 
Published: August 2016

AbstractData-driven phenotype analyses on Electronic Health Record (EHR) data have recently drawn benefits across many areas of clinical practice, uncovering new links in the medical sciences that can potentially affect the well-being of millions of patients. In this paper, EHR data is used to discover novel relationships between diseases by studying their comorbidities (co-occurrences in patients). A novel embedding model is designed to extract knowledge from disease comorbidities by learning from a large-scale EHR database comprising more than 35 million inpatient cases spanning nearly a decade, revealing significant improvements on disease phenotyping over current computational approaches. In addition, the use of the proposed methodology is extended to discover novel disease-gene associations by including valuable domain knowledge from genome-wide association studies. To evaluate our approach, its effectiveness is compared against a held-out set where, again, it revealed very compelling results. For selected diseases, we further identify candidate gene lists for which disease-gene associations were not studied previously. Thus, our approach provides biomedical researchers with new tools to filter genes of interest, thus, reducing costly lab studies.
Thermodynamic and hydrochemical controls on CH4 in a coal seam gas and overlying alluvial aquifer: new insights into CH4 origins
Authors: Owen D. Des. R. , Shouakar-Stash O. , Morgenstern U. , Aravena R. 
Published: August 2016

AbstractUsing a comprehensive data set (dissolved CH4, δ13C-CH4, δ2H-CH4, δ13C-DIC, δ37Cl, δ2H-H2O, δ18O-H2O, Na, K, Ca, Mg, HCO3, Cl, Br, SO4, NO3 and DO), in combination with a novel application of isometric log ratios, this study describes hydrochemical and thermodynamic controls on dissolved CH4 from a coal seam gas reservoir and an alluvial aquifer in the Condamine catchment, eastern Surat/north-western Clarence-Moreton basins, Australia. δ13C-CH4 data in the gas reservoir (−58‰ to −49‰) and shallow coal measures underlying the alluvium (−80‰ to −65‰) are distinct. CO2 reduction is the dominant methanogenic pathway in all aquifers, and it is controlled by SO4 concentrations and competition for reactants such as H2. At isolated, brackish sites in the shallow coal measures and alluvium, highly depleted δ2H-CH4 (<310‰) indicate acetoclastic methanogenesis where SO4 concentrations inhibit CO2 reduction. Evidence of CH4 migration from the deep gas reservoir (200–500 m) to the shallow coal measures (<200 m) or the alluvium was not observed. The study demonstrates the importance of understanding CH4 at different depth profiles within and between aquifers. Further research, including culturing studies of microbial consortia, will improve our understanding of the occurrence of CH4 within and between aquifers in these basins.
Giant Polymersome Protocells Dock with Virus Particle Mimics via Multivalent Glycan-Lectin Interactions
Authors: Kubilis Artur , Abdulkarim Ali , Eissa Ahmed M. , Cameron Neil R. 
Published: August 2016

AbstractDespite the low complexity of their components, several simple physical systems, including microspheres, coacervate droplets and phospholipid membrane structures (liposomes), have been suggested as protocell models. These, however, lack key cellular characteristics, such as the ability to replicate or to dock with extracellular species. Here, we report a simple method for the de novo creation of synthetic cell mimics in the form of giant polymeric vesicles (polymersomes), which are capable of behavior approaching that of living cells. These polymersomes form by self-assembly, under electroformation conditions, of amphiphilic, glycosylated block copolymers in aqueous solution. The glycosylated exterior of the resulting polymeric giant unilamellar vesicles (GUVs) allows their selective interaction with carbohydrate-binding receptor-functionalized particles, in a manner reminiscent of the cell-surface docking of virus particles. We believe that this is the first example of a simple protocell model displaying cell-like behavior through a native receptor-ligand interaction.