bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Fibonacci numbers in lipidomics – Enumerating various classes of fatty acids
Authors: Schuster Stefan , Fichtner Maximilian , Sasso Severin 
Published: January 2017

AbstractIn lipid biochemistry, a fundamental question is how the potential number of fatty acids increases with their chain length. Here, we show that it grows according to the famous Fibonacci numbers when cis/trans isomerism is neglected. Since the ratio of two consecutive Fibonacci numbers tends to the Golden section, 1.618, organisms can increase fatty acid variability approximately by that factor per carbon atom invested. Moreover, we show that, under consideration of cis/trans isomerism and/or of modification by hydroxy and/or oxo groups, diversity can be described by generalized Fibonacci numbers (e.g. Pell numbers). For the sake of easy comprehension, we deliberately build the proof on the recursive definitions of these number series. Our results should be of interest for mass spectrometry, combinatorial chemistry, synthetic biology, patent applications, use of fatty acids as biomarkers and the theory of evolution. The recursive definition of Fibonacci numbers paves the way to construct all structural formulas of fatty acids in an automated way.
Determining the relative contribution of retinal disparity and blur cues to ocular accommodation in Down syndrome
Authors: Doyle Lesley , Saunders Kathryn J. , Little Julie-Anne 
Published: January 2017

AbstractIndividuals with Down syndrome (DS) often exhibit hypoaccommodation alongside accurate vergence. This study investigates the sensitivity of the two systems to retinal disparity and blur cues, establishing the relationship between the two in terms of accommodative-convergence to accommodation (AC/A) and convergence-accommodation to convergence (CA/C) ratios. An objective photorefraction system measured accommodation and vergence under binocular conditions and when retinal disparity and blur cues were removed. Participants were aged 6–16 years (DS n = 41, controls n = 76). Measures were obtained from 65.9% of participants with DS and 100% of controls. Accommodative and vergence responses were reduced with the removal of one or both cues in controls (p < 0.007). For participants with DS, removal of blur was less detrimental to accommodative responses than removal of disparity; accommodative responses being significantly better when all cues were available or when blur was removed in comparison to when proximity was the only available cue. AC/A ratios were larger and CA/C ratios smaller in participants with DS (p < 0.00001). This study demonstrates that retinal disparity is the main driver to both systems in DS and illustrates the diminished influence of retinal blur. High AC/A and low CA/C ratios in combination with disparity-driven responses suggest prioritisation of vergence over accurate accommodation.
Polychlorinated biphenyls target Notch/Dll and VEGF R2 in the mouse placenta and human trophoblast cell lines for their anti-angiogenic effects
Authors: Kalkunte Satyan , Huang Zheping , Lippe Eliana , Kumar Sunil , Robertson Larry W. , Sharma Surendra 
Published: January 2017

AbstractThe intrauterine environment is particularly vulnerable to environmental exposures. We previously established a mouse model that provided evidence for pregnancy complications and placental anti-angiogenesis in response to Aroclor 1254 (A-1254), a mixture of polychlorinated biphenyls (PCBs). Importantly, these effects were observed in IL-10−/−, but not wild type, mice, suggesting that IL-10 deficiency predisposes to pregnancy disruptive effects of environmental toxicants. However, the mechanisms by which PCBs cause anti-angiogenic effects are unclear. Here, we evaluated PCB-mediated anti-angiogenic effects by diverse but complementary approaches, including HUVEC-mediated trophoblast invasion in nude mice, in vitro three-dimensional capillary tube formation involving HUVEC and/or HTR8 trophoblasts, and aortic ring endothelial cell outgrowth/sprouting. Taken together, our data suggest that PCBs act as potent anti-angiogenic agents. Importantly, we show that treatment of pregnant IL-10−/− mice with A-1254 resulted in placental activation of the Notch/Delta-like ligand (Dll) pathway, a master regulator of cell-cell interaction and vascular patterning. Similar results were obtained with HUVEC and HTR8 trophoblasts. Rescue of A-1254-induced disruption of HUVEC-based tube formation by γ-secretase inhibitor L1790 confirmed the critical role of the Notch/Dll pathway. Our data suggest that PCBs impart pregnancy disruptive functions by activating the Notch/Dll pathway and by inducing anti-angiogenic effects at the maternal-fetal interface.
Novel long-chain compounds with both immunomodulatory and MenA inhibitory activities against Staphylococcus aureus and its biofilm
Authors: Choi Seoung-ryoung , Frandsen Joel , Narayanasamy Prabagaran 
Published: January 2017

AbstractMenaquinone (MK) biosynthesis pathway is a potential target for evaluating antimicrobials in gram-positive bacteria. Here, 1,4-dihydroxy-2-naphthoate prenyltransferase (MenA) was targeted to reduce methicillin-resistantStaphylococcus aureus(MRSA) growth. MenA inhibiting, long chain-based compounds were designed, synthesized and evaluated against MRSA and menaquinone utilizing bacteria in aerobic conditions. The results showed that these bacteria were susceptible to most of the compounds. Menaquinone (MK-4) supplementation rescued MRSA growth, suggesting these compounds inhibit MK biosynthesis.3aand7cexhibited promising inhibitory activities with MICs ranging 1–8 μg/mL against MRSA strains. The compounds did not facilitate small colony variant formation. These compounds also inhibited the biofilm growth by MRSA at high concentration. Compounds3a,6band7cdisplayed a promising extracellular bactericidal activity against MRSA at concentrations equal to and four-fold less than their respective MICs. We also observed cytokines released from THP-1 macrophages treated with compounds3a,6band7cand found decreases in TNF-α and IL-6 release and increase in IL-1β. These data provide evidence that MenA inhibitors act as TNF-α and IL-6 inhibitors, raising the potential for development and application of these compounds as potential immunomodulatory agents.
Towards an emotional ‘stress test’: a reliable, non-subjective cognitive measure of anxious responding
Authors: Aylward Jessica , Robinson Oliver J. 
Published: January 2017

AbstractResponse to stress or external threats is a key factor in mood and anxiety disorder aetiology. Current measures of anxious responding to threats are limited because they largely rely on retrospective self-report. Objectively quantifying individual differences in threat response would be a valuable step towards improving our understanding of anxiety disorder vulnerability. Our goal is to therefore develop a reliable, objective, within-subject ‘stress-test’ of anxious responding. To this end, we examined threat-potentiated performance on an inhibitory control task from baseline to 2–4 weeks (n = 50) and again after 5–9 months (n = 22). We also describe single session data for a larger sample (n = 157) to provide better population-level estimates of task performance variance. Replicating previous findings, threat of shock improved distractor accuracy and slowed target reaction time on our task. Critically, both within-subject self-report measures of anxiety (ICC = 0.66) and threat-potentiated task performance (ICC = 0.58) showed clinically useful test-retest reliability. Threat-potentiated task performance may therefore hold promise as a non-subjective measure of individual anxious responding.
Experimental Array for Generating Dual Circularly-Polarized Dual-Mode OAM Radio Beams
Authors: Bai Xu-Dong , Liang Xian-Ling , Sun Yun-Tao , Hu Peng-Cheng , Yao Yu , Wang Kun , Geng Jun-Ping , Jin Rong-Hong 
Published: January 2017

AbstractRecently, vortex beam carrying orbital angular momentum (OAM) for radio communications has attracted much attention for its potential of transmitting multiple signals simultaneously at the same frequency, which can be used to increase the channel capacity. However, most of the methods for getting multi-mode OAM radio beams are of complicated structure and very high cost. This paper provides an effective solution of generating dual circularly-polarized (CP) dual-mode OAM beams. The antenna consists of four dual-CP elements which are sequentially rotated 90 degrees in the clockwise direction. Different from all previous published research relating to OAM generation by phased arrays, the four elements are fed with the same phase for both left-hand circular polarization (LHCP) and right-hand circular polarization (RHCP). The dual-mode operation for OAM is achieved through the opposite phase differences generated for LHCP and RHCP, when the dual-CP elements are sequentially rotated in the clockwise direction. The measured results coincide well with the simulated ones, which verified the effectiveness of the proposed design.
The Content of Imagined Sounds Changes Visual Motion Perception in the Cross-Bounce Illusion
Authors: Berger Christopher C. , Ehrsson H. Henrik 
Published: January 2017

AbstractCan what we imagine hearing change what we see? Whether imagined sensory stimuli are integrated with external sensory stimuli to shape our perception of the world has only recently begun to come under scrutiny. Here, we made use of the cross-bounce illusion in which an auditory stimulus presented at the moment two passing objects meet promotes the perception that the objects bounce off rather than cross by one another to examine whether the content of imagined sound changes visual motion perception in a manner that is consistent with multisensory integration. The results from this study revealed that auditory imagery of a sound with acoustic properties typical of a collision (i.e., damped sound) promoted the bounce-percept, but auditory imagery of the same sound played backwards (i.e., ramped sound) did not. Moreover, the vividness of the participants’ auditory imagery predicted the strength of this imagery-induced illusion. In a separate experiment, we ruled out the possibility that changes in attention (i.e., sensitivity index d′) or response bias (response bias index c) were sufficient to explain this effect. Together, these findings suggest that this imagery-induced multisensory illusion reflects the successful integration of real and imagined cross-modal sensory stimuli, and more generally, that what we imagine hearing can change what we see.
Variation in short-term and long-term responses of photosynthesis and isoprenoid-mediated photoprotection to soil water availability in four Douglas-fir provenances
Authors: Junker Laura Verena , Kleiber Anita , Jansen Kirstin , Wildhagen Henning , Hess Moritz , Kayler Zachary , Kammerer Bernd , Schnitzler Jörg-Peter , Kreuzwieser Jürgen , Gessler Arthur , Ensminger Ingo 
Published: January 2017

AbstractFor long-lived forest tree species, the understanding of intraspecific variation among populations and their response to water availability can reveal their ability to cope with and adapt to climate change. Dissipation of excess excitation energy, mediated by photoprotective isoprenoids, is an important defense mechanism against drought and high light when photosynthesis is hampered. We used 50-year-old Douglas-fir trees of four provenances at two common garden experiments to characterize provenance-specific variation in photosynthesis and photoprotective mechanisms mediated by essential and non-essential isoprenoids in response to soil water availability and solar radiation. All provenances revealed uniform photoprotective responses to high solar radiation, including increased de-epoxidation of photoprotective xanthophyll cycle pigments and enhanced emission of volatile monoterpenes. In contrast, we observed differences between provenances in response to drought, where provenances sustaining higher CO2assimilation rates also revealed increased water-use efficiency, carotenoid-chlorophyll ratios, pools of xanthophyll cycle pigments, β-carotene and stored monoterpenes. Our results demonstrate that local adaptation to contrasting habitats affected chlorophyll-carotenoid ratios, pool sizes of photoprotective xanthophylls, β-carotene, and stored volatile isoprenoids. We conclude that intraspecific variation in isoprenoid-mediated photoprotective mechanisms contributes to the adaptive potential of Douglas-fir provenances to climate change.
Plasma heme-induced renal toxicity is related to a capillary rarefaction
Authors: Tabibzadeh Nahid , Estournet Céline , Placier Sandrine , Perez Joëlle , Bilbault Héloïse , Girshovich Alexis , Vandermeersch Sophie , Jouanneau Chantal , Letavernier Emmanuel , Hammoudi Nadjib , Lionnet François , Haymann Jean-Philippe 
Published: January 2017

AbstractSevere hypertension can lead to malignant hypertension (MH) with renal thrombotic microangiopathy and hemolysis. The role of plasma heme release in this setting is unknown. We aimed at evaluating the effect of a mild plasma heme increase by hemin administration in angiotensin II (AngII)-mediated hypertensive rats. Prevalence of MH and blood pressure values were similar in AngII and AngII + hemin groups. MH rats displayed a decreased renal blood flow (RBF), increased renal vascular resistances (RVR), and increased aorta and interlobar arteries remodeling with a severe renal microcirculation assessed by peritubular capillaries (PTC) rarefaction. Hemin-treated rats with or without AngII displayed also a decreased RBF and increased RVR explained only by PCT rarefaction. In AngII rats, RBF was similar to controls (with increased RVR). PTC density appeared strongly correlated to tubular damage score (rho = −0.65, p < 0.0001) and also renal Heme Oygenase-1 (HO-1) mRNA (rho = −0.67, p < 0.0001). HO-1 was expressed in PTC and renal tubules in MH rats, but only in PTC in other groups. In conclusion, though increased plasma heme does not play a role in triggering or aggravating MH, heme release appears as a relevant toxic mediator leading to renal impairment, primarily through PTC endothelial dysfunction rather than direct tubular toxicity.
Generation of germline ablated male pigs by CRISPR/Cas9 editing of the NANOS2 gene
Authors: Park Ki-Eun , Kaucher Amy V. , Powell Anne , Waqas Muhammad Salman , Sandmaier Shelley E.S. , Oatley Melissa J. , Park Chi-Hun , Tibary Ahmed , Donovan David M. , Blomberg Le Ann , Lillico Simon G. , Whitelaw C. Bruce A. , Mileham Alan , Telugu Bhanu P. , Oatley Jon M. 
Published: January 2017

AbstractGenome editing tools have revolutionized the generation of genetically modified animals including livestock. In particular, the domestic pig is a proven model of human physiology and an agriculturally important species. In this study, we utilized the CRISPR/Cas9 system to edit theNANOS2gene in pig embryos to generate offspring with mono-allelic and bi-allelic mutations. We found thatNANOS2knockout pigs phenocopy knockout mice with male specific germline ablation but other aspects of testicular development are normal. Moreover, male pigs with one intactNANOS2allele and female knockout pigs are fertile. From an agriculture perspective,NANOS2knockout male pigs are expected to serve as an ideal surrogate for transplantation of donor spermatogonial stem cells to expand the availability of gametes from genetically desirable sires.
In-gap corner states in core-shell polygonal quantum rings
Authors: Sitek Anna , Ţolea Mugurel , Niţă Marian , Serra Llorenç , Gudmundsson Vidar , Manolescu Andrei 
Published: January 2017

AbstractWe study Coulomb interacting electrons confined in polygonal quantum rings. We focus on the interplay of localization at the polygon corners and Coulomb repulsion. Remarkably, the Coulomb repulsion allows the formation of in-gap states, i.e., corner-localized states of electron pairs or clusters shifted to energies that were forbidden for non-interacting electrons, but below the energies of corner-side-localized states. We specify conditions allowing optical excitation to those states.
MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes
Authors: Ma Wei , Huang Chuanbo , Zhou Yuan , Li Jianwei , Cui Qinghua 
Published: January 2017

AbstractThe microbiota colonized on human body is renowned as “a forgotten organ” due to its big impacts on human health and disease. Recently, microbiome studies have identified a large number of microbes differentially regulated in a variety of conditions, such as disease and diet. However, methods for discovering biological patterns in the differentially regulated microbes are still limited. For this purpose, here, we developed a web-based tool named MicroPattern to discover biological patterns for a list of microbes. In addition, MicroPattern implemented and integrated an algorithm we previously presented for the calculation of disease similarity based on disease-microbe association data. MicroPattern first grouped microbes into different sets based on the associated diseases and the colonized positions. Then, for a given list of microbes, MicroPattern performed enrichment analysis of the given microbes on all of the microbe sets. Moreover, using MicroPattern, we can also calculate disease similarity based on the shared microbe associations. Finally, we confirmed the accuracy and usefulness of MicroPattern by applying it to the changed microbes under the animal-based diet condition. MicroPattern is freely available at http://www.cuilab.cn/micropattern.
Tomato progeny inherit resistance to the nematode Meloidogyne javanica linked to plant growth induced by the biocontrol fungus Trichoderma atroviride
Authors: Medeiros Hugo Agripino de , Araújo Filho Jerônimo Vieira de , Freitas Leandro Grassi de , Castillo Pablo , Rubio María Belén , Hermosa Rosa , Monte Enrique 
Published: January 2017

AbstractRoot-knot nematodes (RKN) are major crop pathogens worldwide. Trichoderma genus fungi are recognized biocontrol agents and a direct activity of Trichoderma atroviride (Ta) against the RKN Meloidogyne javanica (Mj), in terms of 42% reduction of number of galls (NG), 60% of number of egg masses and 90% of number of adult nematodes inside the roots, has been observed in tomato grown under greenhouse conditions. An in vivo split-root designed experiment served to demonstrate that Ta induces systemic resistance towards Mj, without the need for the organisms to be in direct contact, and significantly reduces NG (20%) and adult nematodes inside tomato roots (87%). The first generation (F1) of Ta-primed tomato plants inherited resistance to RKN; although, the induction of defenses occurred through different mechanisms, and in varying degrees, depending on the Ta-Mj interaction. Plant growth promotion induced by Ta was inherited without compromising the level of resistance to Mj, as the progeny of Ta-primed plants displayed increased size and resistance to Mj without fitness costs. Gene expression results from the defense inductions in the offspring of Ta-primed plants, suggested that an auxin-induced reactive oxygen species production promoted by Ta may act as a major defense strategy during plant growth.
Comparative mitochondrial genomics toward exploring molecular markers in the medicinal fungus Cordyceps militaris
Authors: Zhang Shu , Hao Ai-Jing , Zhao Yu-Xiang , Zhang Xiao-Yu , Zhang Yong-Jie 
Published: January 2017

AbstractCordyceps militarisis a fungus used for developing health food, but knowledge about its intraspecific differentiation is limited due to lack of efficient markers. Herein, we assembled the mitochondrial genomes of eightC. militarisstrains and performed a comparative mitochondrial genomic analysis together with three previously reported mitochondrial genomes of the fungus. Sizes of the 11 mitochondrial genomes varied from 26.5 to 33.9 kb mainly due to variable intron contents (from two to eight introns per strain). Nucleotide variability varied according to different regions with non-coding regions showing higher variation frequency than coding regions. Recombination events were identified between some locus pairs but seemed not to contribute greatly to genetic variations of the fungus. Based on nucleotide diversity fluctuations across the alignment of all mitochondrial genomes, molecular markers with the potential to be used for future typing studies were determined.
High fat diet-induced changes of mouse hepatic transcription and enhancer activity can be reversed by subsequent weight loss
Authors: Siersbæk Majken , Varticovski Lyuba , Yang Shutong , Baek Songjoon , Nielsen Ronni , Mandrup Susanne , Hager Gordon L. , Chung Jay H. , Grøntved Lars 
Published: January 2017

AbstractEpigenetic factors have been suggested to play an important role in metabolic memory by trapping and maintaining initial metabolic changes within the transcriptional regulatory machinery. In this study we fed mice a high fat diet (HFD) for seven weeks followed by additional five weeks of chow, to identify HFD-mediated changes to the hepatic transcriptional program that may persist after weight loss. Mice fed a HFD displayed increased fasting insulin levels, hepatosteatosis and major changes in hepatic gene transcription associated with modulation of H3K27Ac at enhancers, but no significant changes in chromatin accessibility, indicating that HFD-regulated gene transcription is primarily controlled by modulating the activity of pre-established enhancers. After return to the same body weight as chow fed control mice, the fasting insulin, glucose, and hepatic triglyceride levels were fully restored to normal levels. Moreover, HFD-regulated H3K27Ac and mRNA levels returned to similar levels as control mice. These data demonstrates that the transcription regulatory landscape in the liver induced by HFD is highly dynamic and can be reversed by weight loss. This provides hope for efficient treatment of early obesity-associated changes to hepatic complications by simple weight loss intervention without persistent reprograming of the liver transcriptome.
Lytic polysaccharide monooxygenases disrupt the cellulose fibers structure
Authors: Villares Ana , Moreau Céline , Bennati-Granier Chloé , Garajova Sona , Foucat Loïc , Falourd Xavier , Saake Bodo , Berrin Jean-Guy , Cathala Bernard 
Published: January 2017

AbstractLytic polysaccharide monooxygenases (LPMOs) are a class of powerful oxidative enzymes that breakdown recalcitrant polysaccharides such as cellulose. Here we investigate the action of LPMOs on cellulose fibers. After enzymatic treatment and dispersion, LPMO-treated fibers show intense fibrillation. Cellulose structure modifications visualized at different scales indicate that LPMO creates nicking points that trigger the disintegration of the cellulose fibrillar structure with rupture of chains and release of elementary nanofibrils. Investigation of LPMO action using solid-state NMR provides direct evidence of modification of accessible and inaccessible surfaces surrounding the crystalline core of the fibrils. The chains breakage likely induces modifications of the cellulose network and weakens fibers cohesion promoting their disruption. Besides the formation of new initiation sites for conventional cellulases, this work provides the first evidence of the direct oxidative action of LPMOs with the mechanical weakening of the cellulose ultrastructure. LPMOs can be viewed as promising biocatalysts for enzymatic modification or degradation of cellulose fibers.