bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post-transitional adaptation of the left heart in uncomplicated, very preterm infants
Authors: De Waal Koert , Phad Nilkant , Lakkundi Anil , Tan Peter 
Published: January 2017

AbstractBackgroundThe postnatal period in preterm infants involves multiple physiological changes occurring immediately after birth and continuing for days or weeks. To recognise and treat compromise, it is important to measure cardiovascular function. The aim of this study was to describe longitudinal left ventricular function using conventional and novel echocardiography techniques in preterm infants who did not experience significant antenatal or postnatal complications and treatments.MethodsWe prospectively obtained cardiac ultrasound images at days 3, 7, 14, 21, and 28 in 25 uncomplicated, preterm infants <30 weeks of gestation. Speckle tracking analysis of the four chambers and short-axis images provided parameters of left ventricular volume, deformation, and basal myocardial velocities. The patent ductus arteriosus, cardiac dimensions, and atrial volume were also measured.ResultsStroke volume increased by 24% during the study period (1.05–1.30 ml/kg, p<0.05). Cardiac length, diameter, and systolic basal myocardial velocity increased with unchanged wall stress and deformation parameters. Diastolic function parameters resembled that of the fetus with predominance of atrial contraction compared with early diastolic velocities. Blood pressure and estimates of left ventricular filing pressure increased, suggesting that left ventricular compliance did not change in this period.ConclusionStroke volume increased in the first 28 days after preterm birth. The preterm heart adapted by increasing its size, while maintaining systolic and atrial function, independent of early diastolic maturation. Longitudinal deformation of the left ventricle remained unchanged, suggesting relatively preserved function with maturation.
A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements
Authors: Hartmann Fanny E , Sánchez-Vallet Andrea , McDonald Bruce A , Croll Daniel 
Published: January 2017

AbstractFungal pathogens can rapidly evolve virulence towards resistant crops in agricultural ecosystems. Gains in virulence are often mediated by the mutation or deletion of a gene encoding a protein recognized by the plant immune system. However, the loci and the mechanisms of genome evolution enabling rapid virulence evolution are poorly understood. We performed genome-wide association mapping on a global collection of 106 strains of Zymoseptoria tritici, the most damaging pathogen of wheat in Europe, to identify polymorphisms linked to virulence on two wheat varieties. We found 25 distinct genomic loci associated with reproductive success of the pathogen. However, no locus was shared between the host genotypes, suggesting host specialization. The main locus associated with virulence encoded a highly expressed, small secreted protein. Population genomic analyses showed that the gain in virulence was explained by a segregating gene deletion polymorphism. The deletion was likely adaptive by preventing detection of the encoded protein. Comparative genomics of closely related species showed that the locus emerged de novo since speciation. A large cluster of transposable elements in direct proximity to the locus generated extensive rearrangements leading to multiple independent gene losses. Our study demonstrates that rapid turnover in the chromosomal structure of a pathogen can drive host specialization.
Fractal nematic colloids
Authors: Hashemi S. M. , Jagodič U. , Mozaffari M. R. , Ejtehadi M. R. , Muševič I. , Ravnik M. 
Published: January 2017

AbstractFractals are remarkable examples of self-similarity where a structure or dynamic pattern is repeated over multiple spatial or time scales. However, little is known about how fractal stimuli such as fractal surfaces interact with their local environment if it exhibits order. Here we show geometry-induced formation of fractal defect states in Koch nematic colloids, exhibiting fractal self-similarity better than 90% over three orders of magnitude in the length scales, from micrometers to nanometres. We produce polymer Koch-shaped hollow colloidal prisms of three successive fractal iterations by direct laser writing, and characterize their coupling with the nematic by polarization microscopy and numerical modelling. Explicit generation of topological defect pairs is found, with the number of defects following exponential-law dependence and reaching few 100 already at fractal iteration four. This work demonstrates a route for generation of fractal topological defect states in responsive soft matter.
Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast
Authors: Jeffares Daniel C. , Jolly Clemency , Hoti Mimoza , Speed Doug , Shaw Liam , Rallis Charalampos , Balloux Francois , Dessimoz Christophe , Bähler Jürg , Sedlazeck Fritz J. 
Published: January 2017

AbstractLarge structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. We analyse the effects of SVs on gene expression, quantitative traits and intrinsic reproductive isolation in the yeast Schizosaccharomyces pombe. We establish a high-quality curated catalogue of SVs in the genomes of a worldwide library of S. pombe strains, including duplications, deletions, inversions and translocations. We show that copy number variants (CNVs) show a variety of genetic signals consistent with rapid turnover. These transient CNVs produce stoichiometric effects on gene expression both within and outside the duplicated regions. CNVs make substantial contributions to quantitative traits, most notably intracellular amino acid concentrations, growth under stress and sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases.
Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness
Authors: Nishita Michiru , Park Seung-Yeol , Nishio Tadashi , Kamizaki Koki , Wang ZhiChao , Tamada Kota , Takumi Toru , Hashimoto Ryuju , Otani Hiroki , Pazour Gregory J. , Hsu Victor W. , Minami Yasuhiro 
Published: January 2017

AbstractSignaling through the Ror2 receptor tyrosine kinase promotes invadopodia formation for tumor invasion. Here, we identify intraflagellar transport 20 (IFT20) as a new target of this signaling in tumors that lack primary cilia, and find that IFT20 mediates the ability of Ror2 signaling to induce the invasiveness of these tumors. We also find that IFT20 regulates the nucleation of Golgi-derived microtubules by affecting the GM130-AKAP450 complex, which promotes Golgi ribbon formation in achieving polarized secretion for cell migration and invasion. Furthermore, IFT20 promotes the efficiency of transport through the Golgi complex. These findings shed new insights into how Ror2 signaling promotes tumor invasiveness, and also advance the understanding of how Golgi structure and transport can be regulated.
CD5 molecule-like and transthyretin as putative biomarkers of chronic myeloid leukemia - an insight from the proteomic analysis of human plasma
Authors: Fatima Iram , Sadaf Saima , Musharraf Syed Ghulam , Hashmi Naghma , Akhtar Muhammad Waheed 
Published: January 2017

AbstractBetter and sensitive biomarkers are needed to help understand the mechanism of disease onset, progression, prognosis and monitoring of the therapeutic response. Aim of this study was to identify the candidate circulating markers of chronic-phase chronic myeloid leukemia (CP-CML) manifestations, having potential to develop into predictive- or monitoring-biomarkers. A proteomic approach, two-dimensional gel electrophoresis in conjunction with mass spectrometry (2DE-MS), was employed for this purpose. Based on the spot intensity measurements, six proteins were found to be consistently dysregulated in CP-CML subjects compared to the healthy controls [false discovery rate (FDR) threshold ≤0.05]. These were identified as α-1-antichymotrypsin, α-1-antitrypsin, CD5 molecule-like, stress-induced phosphoprotein 1, vitamin D binding protein isoform 1 and transthyretin by MS analysis [PMF score ≥79; data accessible via ProteomeXchange with identifier PXD002757]. Quantitative ELISA, used for validation of candidate proteins both in the pre-treated and nilotinib-treated CP-CML cases, demonstrate that CD5 molecule-like, transthyretin and alpha-1-antitrypsin may serve as useful predictive markers and aid in monitoring the response of TKI-based therapy (ANOVA p < 0.0001). Two of the circulating marker proteins, identified in this study, had not previously been associated with chronic- or acute-phase myeloid leukemia. Exploration of their probable association with CP-CML, in a larger study cohort, may add to our understanding of the disease mechanism besides developing clinically useful biomarkers in future.
A systematic SNP selection approach to identify mechanisms underlying disease aetiology: linking height to post-menopausal breast and colorectal cancer risk
Authors: Elands Rachel J. J. , Simons Colinda C. J. M. , Riemenschneider Mona , Isaacs Aaron , Schouten Leo J. , Verhage Bas A. , Van Steen Kristel , Godschalk Roger W. L. , van den Brandt Piet A. , Stoll Monika , Weijenberg Matty P. 
Published: January 2017

AbstractData from GWAS suggest that SNPs associated with complex diseases or traits tend to co-segregate in regions of low recombination, harbouring functionally linked gene clusters. This phenomenon allows for selecting a limited number of SNPs from GWAS repositories for large-scale studies investigating shared mechanisms between diseases. For example, we were interested in shared mechanisms between adult-attained height and post-menopausal breast cancer (BC) and colorectal cancer (CRC) risk, because height is a risk factor for these cancers, though likely not a causal factor. Using SNPs from public GWAS repositories at p-values < 1 × 10−5 and a genomic sliding window of 1 mega base pair, we identified SNP clusters including at least one SNP associated with height and one SNP associated with either post-menopausal BC or CRC risk (or both). SNPs were annotated to genes using HapMap and GRAIL and analysed for significantly overrepresented pathways using ConsensuspathDB. Twelve clusters including 56 SNPs annotated to 26 genes were prioritised because these included at least one height- and one BC risk- or CRC risk-associated SNP annotated to the same gene. Annotated genes were involved in Indian hedgehog signalling (p-value = 7.78 × 10−7) and several cancer site-specific pathways. This systematic approach identified a limited number of clustered SNPs, which pinpoint potential shared mechanisms linking together the complex phenotypes height, post-menopausal BC and CRC.
Beta-agonist stimulation ameliorates the phenotype of spinal and bulbar muscular atrophy mice and patient-derived myotubes
Authors: Milioto Carmelo , Malena Adriana , Maino Eleonora , Polanco Maria J. , Marchioretti Caterina , Borgia Doriana , Pereira Marcelo Gomes , Blaauw Bert , Lieberman Andrew P. , Venturini Roberta , Plebani Mario , Sambataro Fabio , Vergani Lodovica , Pegoraro Elena , Sorarù Gianni , Pennuto Maria 
Published: January 2017

AbstractSpinal and bulbar muscular atrophy (SBMA) is a neuromuscular disease characterized by the loss of lower motor neurons. SBMA is caused by expansions of a polyglutamine tract in the gene coding for androgen receptor (AR). Expression of polyglutamine-expanded AR causes damage to motor neurons and skeletal muscle cells. Here we investigated the effect of β-agonist stimulation in SBMA myotube cells derived from mice and patients, and in knock-in mice. We show that treatment of myotubes expressing polyglutamine-expanded AR with the β-agonist clenbuterol increases their size. Clenbuterol activated the phosphatidylinositol-3-kinase (PI3K)/Akt/mechanistic target of rapamycin (mTOR) pathway and decreased the accumulation of polyglutamine-expanded AR. Treatment of SBMA knock-in mice with clenbuterol, which was started at disease onset, ameliorated motor function and extended survival. Clenbuterol improved muscle pathology, attenuated the glycolytic-to-oxidative metabolic alterations occurring in SBMA muscles and induced hypertrophy of both glycolytic and oxidative fibers. These results indicate that β-agonist stimulation is a novel therapeutic strategy for SBMA.
Body size and vocalization in primates and carnivores
Authors: Bowling D. L. , Garcia M. , Dunn J. C. , Ruprecht R. , Stewart A. , Frommolt K.-H. , Fitch W. T. 
Published: January 2017

AbstractA fundamental assumption in bioacoustics is that large animals tend to produce vocalizations with lower frequencies than small animals. This inverse relationship between body size and vocalization frequencies is widely considered to be foundational in animal communication, with prominent theories arguing that it played a critical role in the evolution of vocal communication, in both production and perception. A major shortcoming of these theories is that they lack a solid empirical foundation: rigorous comparisons between body size and vocalization frequencies remain scarce, particularly among mammals. We address this issue here in a study of body size and vocalization frequencies conducted across 91 mammalian species, covering most of the size range in the orders Primates (n = 50; ~0.11–120 Kg) and Carnivora (n = 41; ~0.14–250 Kg). We employed a novel procedure designed to capture spectral variability and standardize frequency measurement of vocalization data across species. The results unequivocally demonstrate strong inverse relationships between body size and vocalization frequencies in primates and carnivores, filling a long-standing gap in mammalian bioacoustics and providing an empirical foundation for theories on the adaptive function of call frequency in animal communication.
Candidate pheromone receptors of codling moth Cydia pomonella respond to pheromones and kairomones
Authors: Cattaneo Alberto Maria , Gonzalez Francisco , Bengtsson Jonas M. , Corey Elizabeth A. , Jacquin-Joly Emmanuelle , Montagné Nicolas , Salvagnin Umberto , Walker William B. , Witzgall Peter , Anfora Gianfranco , Bobkov Yuriy V. 
Published: January 2017

AbstractOlfaction plays a dominant role in the mate-finding and host selection behaviours of the codling moth (Cydia pomonella), an important pest of apple, pear and walnut orchards worldwide. Antennal transcriptome analysis revealed a number of abundantly expressed genes related to the moth olfactory system, including those encoding the olfactory receptors (ORs) CpomOR1, CpomOR3 and CpomOR6a, which belong to the pheromone receptor (PR) lineage, and the co-receptor (CpomOrco). Using heterologous expression, in both Drosophila olfactory sensory neurones and in human embryonic kidney cells, together with electrophysiological recordings and calcium imaging, we characterize the basic physiological and pharmacological properties of these receptors and demonstrate that they form functional ionotropic receptor channels. Both the homomeric CpomOrco and heteromeric CpomOrco + OR complexes can be activated by the common Orco agonists VUAA1 and VUAA3, as well as inhibited by the common Orco antagonists amiloride derivatives. CpomOR3 responds to the plant volatile compound pear ester ethyl-(E,Z)-2,4-decadienoate, while CpomOR6a responds to the strong pheromone antagonist codlemone acetate (E,E)-8,10-dodecadien-1-yl acetate. These findings represent important breakthroughs in the deorphanization of codling moth pheromone receptors, as well as more broadly into insect ecology and evolution and, consequently, for the development of sustainable pest control strategies based on manipulating chemosensory communication.
Differential growth of the northern Tibetan margin: evidence for oblique stepwise rise of the Tibetan Plateau
Authors: Wang Fei , Shi Wenbei , Zhang Weibin , Wu Lin , Yang Liekun , Wang Yinzhi , Zhu Rixiang 
Published: January 2017

AbstractModels of how high elevations formed across Tibet predict: (a) the continuous thickening of a “viscous sheet”; (b) time-dependent, oblique stepwise growth; and (c) synchronous deformation across Tibet that accompanied collision. Our new observations may shed light on this issue. Here, we use 40Ar/39Ar and (U-Th)/He thermochronology from massifs in the hanging walls of thrust structures along the Kunlun Belt, the first-order orogenic range at the northern Tibetan margin, to elucidate the exhumation history. The results show that these massifs, and hence the plateau margin, were subject to slow, steady exhumation during the Early Cenozoic, followed by a pulse of accelerated exhumation during 40–35 Ma. The exhumation rate increases westward (from ~0.22 to 0.34 and 0.5 mm/yr). The two-fold increase in exhumation in the western part (0.5 mm/yr) compared to the eastern part suggests westward increases in exhumation and compressional stress along the Kunlun Belt. We relate these observations to the mechanisms responsible for the oblique stepwise rise of Tibet. After collision, oblique subduction beneath Kunlun caused stronger compressional deformation in the western part than in the eastern part, resulting in differential growth and lateral extrusion.
Charge transport in nanoscale vertical organic semiconductor pillar devices
Authors: Wilbers Janine G. E. , Xu Bojian , Bobbert Peter A. , de Jong Michel P. , van der Wiel Wilfred G. 
Published: January 2017

AbstractWe report charge transport measurements in nanoscale vertical pillar structures incorporating ultrathin layers of the organic semiconductor poly(3-hexylthiophene) (P3HT). P3HT layers with thickness down to 5 nm are gently top-contacted using wedging transfer, yielding highly reproducible, robust nanoscale junctions carrying high current densities (up to 106 A/m2). Current-voltage data modeling demonstrates excellent hole injection. This work opens up the pathway towards nanoscale, ultrashort-channel organic transistors for high-frequency and high-current-density operation.
Identification of consensus biomarkers for predicting non-genotoxic hepatocarcinogens
Authors: Huang Shan-Han , Tung Chun-Wei 
Published: January 2017

AbstractThe assessment of non-genotoxic hepatocarcinogens (NGHCs) is currently relying on two-year rodent bioassays. Toxicogenomics biomarkers provide a potential alternative method for the prioritization of NGHCs that could be useful for risk assessment. However, previous studies using inconsistently classified chemicals as the training set and a single microarray dataset concluded no consensus biomarkers. In this study, 4 consensus biomarkers of A2m, Ca3, Cxcl1, and Cyp8b1 were identified from four large-scale microarray datasets of the one-day single maximum tolerated dose and a large set of chemicals without inconsistent classifications. Machine learning techniques were subsequently applied to develop prediction models for NGHCs. The final bagging decision tree models were constructed with an average AUC performance of 0.803 for an independent test. A set of 16 chemicals with controversial classifications were reclassified according to the consensus biomarkers. The developed prediction models and identified consensus biomarkers are expected to be potential alternative methods for prioritization of NGHCs for further experimental validation.
Whole-exome sequencing of 228 patients with sporadic Parkinson’s disease
Authors: Sandor Cynthia , Honti Frantisek , Haerty Wilfried , Szewczyk-Krolikowski Konrad , Tomlinson Paul , Evetts Sam , Millin Stephanie , Keane Thomas , McCarthy Shane A. , Durbin Richard , Talbot Kevin , Hu Michele , Webber Caleb , Ponting Chris P. , Wade-Martins Richard 
Published: January 2017

AbstractParkinson’s disease (PD) is the most common neurodegenerative movement disorder, affecting 1% of the population over 65 years characterized clinically by both motor and non-motor symptoms accompanied by the preferential loss of dopamine neurons in the substantia nigra pars compacta. Here, we sequenced the exomes of 244 Parkinson’s patients selected from the Oxford Parkinson’s Disease Centre Discovery Cohort and, after quality control, 228 exomes were available for analyses. The PD patient exomes were compared to 884 control exomes selected from the UK10K datasets. No single non-synonymous (NS) single nucleotide variant (SNV) nor any gene carrying a higher burden of NS SNVs was significantly associated with PD status after multiple-testing correction. However, significant enrichments of genes whose proteins have roles in the extracellular matrix were amongst the top 300 genes with the most significantly associated NS SNVs, while regions associated with PD by a recent Genome Wide Association (GWA) study were enriched in genes containing PD-associated NS SNVs. By examining genes within GWA regions possessing rare PD-associated SNVs, we identified RAD51B. The protein-product of RAD51B interacts with that of its paralogue RAD51, which is associated with congenital mirror movements phenotypes, a phenotype also comorbid with PD.
UV and visible light photocatalytic activity of Au/TiO2 nanoforests with Anatase/Rutile phase junctions and controlled Au locations
Authors: Yu Yang , Wen Wei , Qian Xin-Yue , Liu Jia-Bin , Wu Jin-Ming 
Published: January 2017

AbstractTo magnify anatase/rutile phase junction effects through appropriate Au decorations, a facile solution-based approach was developed to synthesize Au/TiO2 nanoforests with controlled Au locations. The nanoforests cons®isted of anatase nanowires surrounded by radially grown rutile branches, on which Au nanoparticles were deposited with preferred locations controlled by simply altering the order of the fabrication step. The Au-decoration increased the photocatalytic activity under the illumination of either UV or visible light, because of the beneficial effects of either electron trapping or localized surface plasmon resonance (LSPR). Gold nanoparticles located preferably at the interface of anatase/rutile led to a further enhanced photocatalytic activity. The appropriate distributions of Au nanoparticles magnify the beneficial effects arising from the anatase/rutile phase junctions when illuminated by UV light. Under the visible light illumination, the LSPR effect followed by the consecutive electron transfer explains the enhanced photocatalysis. This study provides a facile route to control locations of gold nanoparticles in one-dimensional nanostructured arrays of multiple-phases semiconductors for achieving a further increased photocatalytic activity.