bluuebunny/crossref_metadata_2025_split huggingface dataset:
The susceptibility of sea-island cotton recombinant inbred lines to Fusarium oxysporum f. sp. vasinfectum infection is characterized by altered expression of long noncoding RNAs
Authors: Yao Zhengpei , Chen Quanjia , Chen Dong , Zhan Leilei , Zeng Kai , Gu Aixing , Zhou Jian , Zhang Yu , Zhu Yafu , Gao Wenwei , Wang Liping , Zhang Yi , Qu Yanying 
Published: February 2019

AbstractDisease resistance is one of the most complicated yet important plant traits. The potential functions of long noncoding RNAs (lncRNAs) in response to pathogenic fungi remain unclear. In this study, we sequenced the transcriptomes of four different sea-island cotton (Gossypium barbadense) recombinant inbred lines (RILs) with susceptible, highly susceptible, highly resistant, or super highly resistant phenotypes and compared their responses to Fusarium oxysporum f. sp. vasinfectum (Fov) infection with those of their susceptible and resistant parents. Infection-induced protein coding genes were highly enriched in similar disease resistance-related pathways regardless of fungal susceptibility. In contrast, we found that the expression of a large number of Fov infection-induced lncRNAs was positively correlated with plant susceptibility. Bioinformatics analysis of potential target mRNAs of lncRNAs with both trans-acting and cis-acting mechanisms showed that mRNAs co-expressed or co-located with Fov-regulated lncRNAs were highly enriched in disease resistance-related pathways, including glutathione metabolism, glycolysis, plant hormone signal transduction, anthocyanin biosynthesis, and butanoate metabolism. Together these results suggest that lncRNAs could play a significant role in the response to pathogenic fungal infection and the establishment of disease resistance. The transcriptional regulation of these infection-susceptible lncRNAs could be coordinated with infection-susceptible mRNAs and integrated into a regulatory network to modulate plant-pathogen interactions and disease resistance. Fov-susceptible lncRNAs represent a novel class of molecular markers for breeding of Fov-resistant cotton cultivars.
Genome survey, high-resolution genetic linkage map construction, growth-related quantitative trait locus (QTL) identification and gene location in Scylla paramamosain
Authors: Zhao Ming , Wang Wei , Chen Wei , Ma Chunyan , Zhang Fengying , Jiang Keji , Liu Junguo , Diao Le , Qian Heng , Zhao Junxia , Wang Tian , Ma Lingbo 
Published: February 2019

AbstractScylla paramamosain is one of the most economically important crabs in China. In this study, the first genome survey sequencing of this crab was performed, and the results revealed that the estimated genome size was 1.21 Gb with high heterozygosity (1.3%). Then, RAD technology was used to construct a high-resolution linkage map for this species. A total of 24,444 single nucleotide polymorphism (SNP) makers were grouped into 47 linkage groups. The total length of the linkage groups was 3087.53 cM with a markers interval of 0.92 cM. With the aid of transcriptome and genome scaffold data, 4,271 markers were linked to genes, including several important growth-related genes such as transforming growth factor-beta regulator I, immune related-gene C-type lectin and ecdysone pathway gene broad-complex-like protein. Further, 442 markers, representing 279 QTLs, associated with 24 traits were identified, and of these markers, 78 were linked to genes. Some interesting genes, such as dedicator of cytokinesis protein 3, tenascin-X and DNA helicase MCM8, were believed to have important relationship with specific traits and merit further exploration. The results of this study will accelerate the genetic improvement and genome sequencing analysis of the mud crab.
Growth of vanadium dioxide thin films on hexagonal boron nitride flakes as transferrable substrates
Authors: Genchi Shingo , Yamamoto Mahito , Shigematsu Koji , Aritomi Shodai , Nouchi Ryo , Kanki Teruo , Watanabe Kenji , Taniguchi Takashi , Murakami Yasukazu , Tanaka Hidekazu 
Published: February 2019

AbstractVanadium dioxide (VO2) is an archetypal metal-insulator transition (MIT) material, which has been known for decades to show an orders-of-magnitude change in resistivity across the critical temperature of approximately 340 K. In recent years, VO2 has attracted increasing interest for electronic and photonic applications, along with advancement in thin film growth techniques. Previously, thin films of VO2 were commonly grown on rigid substrates such as crystalline oxides and bulk semiconductors, but the use of transferrable materials as the growth substrates can provide versatility in applications, including transparent and flexible devices. Here, we employ single-crystalline hexagonal boron nitride (hBN), which is an insulating layered material, as a substrate for VO2 thin film growth. VO2 thin films in the polycrystalline form are grown onto hBN thin flakes exfoliated onto silicon (Si) with a thermal oxide, with grains reaching up-to a micrometer in size. The VO2 grains on hBN are orientated preferentially with the (110) surface of the rutile structure, which is the most energetically favorable. The VO2 film on hBN shows a MIT at approximately 340 K, across which the resistivity changes by nearly three orders of magnitude, comparable to VO2 films grown on common substrates such as sapphire and titanium dioxide. The VO2/hBN stack can be picked up from the supporting Si and transferred onto arbitrary substrates, onto which VO2 thin films cannot be grown directly. Our results pave the way for new possibilities for practical and versatile applications of VO2 thin films in electronics and photonics.
Hydration shell differentiates folded and disordered states of a Trp-cage miniprotein, allowing characterization of structural heterogeneity by wide-line NMR measurements
Authors: Taricska Nóra , Bokor Mónika , Menyhárd Dóra K. , Tompa Kálmán , Perczel András 
Published: February 2019

AbstractHydration properties of folded and unfolded/disordered miniproteins were monitored in frozen solutions by wide-line 1H-NMR. The amount of mobile water as function of T (−80 °C < T < 0 °C) was found characteristically different for folded (TC5b), semi-folded (pH < 3, TCb5(H+)) and disordered (TC5b_N1R) variants. Comparing results of wide-line 1H-NMR and molecular dynamics simulations we found that both the amount of mobile water surrounding proteins in ice, as well as their thaw profiles differs significantly as function of the compactness and conformational heterogeneity of their structure. We found that (i) at around −50 °C ~50 H2Os/protein melt (ii) if the protein is well-folded then this amount of mobile water remains quasi-constant up to −20 °C, (iii) if disordered then the quantity of the lubricating mobile water increases with T in a constant manner up to ~200 H2Os/protein by reaching −20 °C. Especially in the −55 °C ↔ −15 °C temperature range, wide-line 1H-NMR detects the heterogeneity of protein fold, providing the size of the hydration shell surrounding the accessible conformers at a given temperature. Results indicate that freezing of protein solutions proceeds by the gradual selection of the enthalpically most favored states that also minimize the number of bridging waters.
The Effect of Visual Capture Towards Subjective Embodiment Within the Full Body Illusion
Authors: Carey Mark , Crucianelli Laura , Preston Catherine , Fotopoulou Aikaterini 
Published: February 2019

AbstractTypically, multisensory illusion paradigms emphasise the importance of synchronous visuotactile integration to induce subjective embodiment towards another body. However, the extent to which embodiment is due to the ‘visual capture’ of congruent visuoproprioceptive information alone remains unclear. Thus, across two experiments (total N = 80), we investigated how mere visual observation of a mannequin body, viewed from a first-person perspective, influenced subjective embodiment independently from concomitant visuotactile integration. Moreover, we investigated whether slow, affective touch on participants’ own, unseen body (without concomitant touch on the seen mannequin) disrupted visual capture effects to a greater degree than fast, non-affective touch. In total, 40% of participants experienced subjective embodiment towards the mannequin body following mere visual observation, and this effect was significantly higher than conditions which included touch to participants own, unseen body. The velocity of the touch that participants received (affective/non-affective) did not differ in modulating visual capture effects. Furthermore, the effects of visual capture and perceived pleasantness of touch was not modulated by subthreshold eating disorder psychopathology. Overall, this study suggests that congruent visuoproprioceptive cues can be sufficient to induce subjective embodiment of a whole body, in the absence of visuotactile integration and beyond mere confabulatory responses.
Differential epithelial and stromal protein profiles in cone and non-cone regions of keratoconus corneas
Authors: Yam Gary Hin-Fai , Fuest Matthias , Zhou Lei , Liu Yu-Chi , Deng Lu , Chan Anita Sook-Yee , Ong Hon Shing , Khor Wei-Boon , Ang Marcus , Mehta Jodhbir S. 
Published: February 2019

AbstractKeratoconus (KC) is an ectatic corneal disease characterized by progressive thinning and irregular astigmatism, and a leading indication for corneal transplantation. KC-associated changes have been demonstrated for the entire cornea, but the pathological thinning and mechanical weakening is usually localized. We performed quantitative proteomics using Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectrometry (SWATH-MS) to analyze epithelial and stromal changes between the topographically-abnormal cone and topographically-normal non-cone regions of advanced KC corneas, compared to age-matched normal corneas. Expression of 20 epithelial and 14 stromal proteins was significantly altered (≥2 or ≤0.5-fold) between cone and non-cone in all 4 KC samples. Ingenuity pathway analysis illustrated developmental and metabolic disorders for the altered epithelial proteome with mitochondrion as the significant gene ontology (GO) term. The differential stromal proteome was related to cellular assembly, tissue organization and connective tissue disorders with endoplasmic reticulum protein folding as the significant GO term. Validation of selected protein expression was performed on archived KC, non-KC and normal corneal specimens by immunohistochemistry. This is the first time to show that KC-associated proteome changes were not limited to the topographically-thinner and mechanically-weakened cone but also non-cone region with normal topography, indicating a peripheral involvement in KC development.
Anti-coccidial properties and mechanisms of an edible herb, Bidens pilosa, and its active compounds for coccidiosis
Authors: Yang Wen-Chin , Yang Cheng-Ying , Liang Yu-Chuan , Yang Chu-Wen , Li Wei-Qun , Chung Chih-Yao , Yang Meng-Ting , Kuo Tien-Fen , Lin Chuen-Fu , Liang Chih-Lung , Chang Cicero Lee-Tian 
Published: February 2019

AbstractAvian coccidiosis is an economically important disease in the poultry industry. In view of the disadvantages of anti-coccidial drugs in chickens, edible plants and their compounds are re-emerging as an alternative strategy to combat this disease. A previous publication reported that the edible plant B. pilosa showed promise for use against coccidiosis. Here, we first investigated into the anti-coccidial effects of B. pilosa. We found that B. pilosa at 100 ppm or more significantly suppressed E. tenella as evidenced by reduction in mortality rate, oocyst excretion and gut pathological severity in chickens and its minimum prophylactic duration was 3 days. Next, we explored the mode of action of anti-coccidial mechanism of B. pilosa. The E. tenella oocysts were not directly killed by B. pilosa; however, administration of the plant suppressed oocyst sporulation, sporozoite invasion, and schizonts in the life cycle of E. tenella. Besides, B. pilosa boosted T cell-mediated immunity. Finally, we characterized the related anti-coccidial phytochemicals and their mode of action. One of three potent polyynes present in B. pilsoa, Compound 1 (cytopiloyne), acted against coccidiosis in chickens in a similar manner to B. pilosa. These data illustrate the anti-coccidial potency and mechanism of B. pilosa and one of its active compounds, and provide a cornerstone for development of novel herbal remedies for avian coccidiosis.
Serum Polyunsaturated Fatty Acids Correlate with Serum Cytokines and Clinical Disease Activity in Crohn’s Disease
Authors: Scoville Elizabeth A. , Allaman Margaret M. , Adams Dawn W. , Motley Amy K. , Peyton Shannon C. , Ferguson Sarah L. , Horst Sara N. , Williams Christopher S. , Beaulieu Dawn B. , Schwartz David A. , Wilson Keith T. , Coburn Lori A. 
Published: February 2019

AbstractCrohn’s disease (CD) has been associated with an increased consumption of n-6 polyunsaturated fatty acid (PUFA), while greater intake of n-3 PUFA has been associated with a reduced risk. We sought to investigate serum fatty acid composition in CD, and associations of fatty acids with disease activity, cytokines, and adipokines. Serum was prospectively collected from 116 CD subjects and 27 non-IBD controls. Clinical disease activity was assessed by the Harvey Bradshaw Index (HBI). Serum fatty acids were measured by gas chromatography. Serum cytokines and adipokines were measured by Luminex assay. Dietary histories were obtained from a subset of patients. Nine serum cytokines and adipokines were increased in CD versus controls. CD subjects had increased percentage serum monounsaturated fatty acids (MUFA), dihomo-gamma linolenic acid (DGLA), eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA), and oleic acid, but decreased arachidonic acid (AA) versus controls. The % total n-3 fatty acids and % EPA directly correlated with pro-inflammatory cytokine levels and HBI, whereas the % total n-6 fatty acids were inversely correlated with pro-inflammatory cytokine levels and HBI. CD subjects had increased caloric intake versus controls, but no alterations in total fat or PUFA intake. We found differences in serum fatty acids, most notably PUFA, in CD that correlated both with clinical disease activity and inflammatory cytokines. Our findings indicate that altered fatty acid metabolism or utilization is present in CD and is related to disease activity.
Integrated single-base resolution maps of transcriptome, sRNAome and methylome of Tomato yellow leaf curl virus (TYLCV) in tomato
Authors: Piedra-Aguilera Álvaro , Jiao Chen , Luna Ana P. , Villanueva Francisco , Dabad Marc , Esteve-Codina Anna , Díaz-Pendón Juan A. , Fei Zhangjun , Bejarano Eduardo R. , Castillo Araceli G. 
Published: February 2019

AbstractGeminiviruses are plant ssDNA viruses that replicate through dsDNA intermediates and form minichromosomes which carry the same epigenetic marks as the host chromatin. During the infection, geminiviruses are targets of the post-transcriptional and transcriptional gene silencing machinery. To obtain insights into the connection between virus-derived small RNAs (vsRNAs), viral genome methylation and gene expression, we obtained the transcriptome, sRNAome and methylome from the geminivirusTomato yellow leaf curl virus-infected tomato plants. The results showed accumulation of transcripts just at the viral ORFs, while vsRNAs spanned the entire genome, showing a prevalent accumulation at regions where the viral ORFs overlapped. The viral genome was not homogenously methylated showing two highly methylated regions located in the C1 ORF and around the intergenic region (IR). The compilation of those results showed a partial correlation between vsRNA accumulation, gene expression and DNA methylation. We could distinguish different epigenetic scenarios along the viral genome, suggesting that in addition to its function as a plant defence mechanism, DNA methylation could have a role in viral gene regulation. To our knowledge, this is the first report that shows integrative single-nucleotide maps of DNA methylation, vsRNA accumulation and gene expression from a plant virus.
Discordant attributes of structural and functional brain connectivity in a two-layer multiplex network
Authors: Lim Sol , Radicchi Filippo , van den Heuvel Martijn P. , Sporns Olaf 
Published: February 2019

AbstractSeveral studies have suggested that functional connectivity (FC) is constrained by the underlying structural connectivity (SC) and mutually correlated. However, not many studies have focused on differences in the network organization of SC and FC, and on how these differences may inform us about their mutual interaction. To explore this issue, we adopt a multi-layer framework, with SC and FC, constructed using Magnetic Resonance Imaging (MRI) data from the Human Connectome Project, forming a two-layer multiplex network. In particular, we examine node strength assortativity within and between the SC and FC layer. We find that, in general, SC is organized assortatively, indicating brain regions are on average connected to other brain regions with similar node strengths. On the other hand, FC shows disassortative mixing. This discrepancy is apparent also among individual resting-state networks within SC and FC. In addition, these patterns show lateralization, with disassortative mixing within FC subnetworks mainly driven from the left hemisphere. We discuss our findings in the context of robustness to structural failure, and we suggest that discordant and lateralized patterns of associativity in SC and FC may provide clues to understand laterality of some neurological dysfunctions and recovery.
(p)ppGpp-mediated stress response induced by defects in outer membrane biogenesis and ATP production promotes survival in Escherichia coli
Authors: Roghanian Mohammad , Semsey Szabolcs , Løbner-Olesen Anders , Jalalvand Farshid 
Published: February 2019

AbstractCellular growth requires a high level of coordination to ensure that all processes run in concert. The role of the nucleotide alarmone (p)ppGpp has been extensively studied in response to external stresses, such as amino acid starvation, in Escherichia coli, but much less is known about the involvement of (p)ppGpp in response to perturbations in intracellular processes. We therefore employed CRISPRi to transcriptionally repress essential genes involved in 14 vital processes and investigated whether a (p)ppGpp-mediated response would be induced. We show that (p)ppGpp is produced and required for a pertinent stress response during interference with outer membrane biogenesis and ADP synthesis specifically. When these processes were perturbed via the transcriptional repression of essential genes, wild type E. coli MG1655 ceased growing and entered a semi-dormant state, whereas isogenic (p)ppGpp0 cells continued to grow uncontrollably to the point of lysis. Furthermore, in vivo measurements revealed that the ATP levels were intrinsically offset in (p)ppGpp0 cells, further indicating a role for the alarmone in cellular energy homeostasis. In summary, our investigation suggests that (p)ppGpp acts as a coordinator of cell growth in response to imbalances in outer membrane biogenesis and adenosine ribonucleotide synthesis, elucidating novel roles for (p)ppGpp in bacterial physiology.
A Novel Optical Scanning Technique with an Inclined Focusing Plane
Authors: Alexandrov Andrey , De Lellis Giovanni , Tioukov Valeri 
Published: February 2019

AbstractWe propose a novel technique for fully automated optical scanning of thin samples. We analyze its performance and estimate the achievable scanning speed to compare it with conventional techniques. It paves the way to the next generation of highspeed scalable scanning systems, at least one order of magnitude faster than existing ones. We show that the efficiency and the accuracy of this new technique are comparable to those of the conventional ones, while the scanning speed scales proportionally with the number of cameras installed, hence the large expected improvement.
Boron-neutron Capture on Activated Carbon for Hydrogen Storage
Authors: Romanos Jimmy , Beckner Matthew , Prosniewski Matthew , Rash Tyler , Lee Mark , Robertson J. David , Firlej Lucyna , Kuchta Bogdan , Pfeifer Peter 
Published: February 2019

AbstractThis work investigates the effects of neutron irradiation on nitrogen and hydrogen adsorption in boron-doped activated carbon. Boron-neutron capture generates an energetic lithium nucleus, helium nucleus, and gamma photons, which can alter the surface and structure of pores in activated carbon. The defects introduced by fission tracks are modeled assuming the slit-shaped pores geometry. Sub-critical nitrogen adsorption shows that nitrogen molecules cannot probe the defects created by fission tracks. Hydrogen adsorption isotherms of irradiated samples indicate higher binding energies compared to their non-irradiated parent samples.
Ibudilast sensitizes glioblastoma to temozolomide by targeting Macrophage Migration Inhibitory Factor (MIF)
Authors: Ha Wendy , Sevim-Nalkiran Hatice , Zaman Ashraf M. , Matsuda Kazuko , Khasraw Mustafa , Nowak Anna K. , Chung Liping , Baxter Robert C. , McDonald Kerrie L. 
Published: February 2019

AbstractRecurrence in patients with glioblastoma (GBM) is inevitable resulting in short survival times, even in patients with O-6-Methylguanine-DNA Methyltransferase (MGMT) methylation. Other pathways must be activated to escape from temozolomide (TMZ) treatment, however acquired resistance mechanisms to TMZ are not well understood. Herein, frozen tumors from 36 MGMT methylated patients grouped according to overall survival were extracted and proteins were profiled using surface-enhanced laser desorption/ionization (SELDI) with time-of flight (TOF) proteomics to identify low molecular weight proteins that associated with poor survival outcomes. Overexpression of macrophage migration inhibitory factor (MIF) was identified in human GBM specimens that were MGMT methylated but showed poor survival. This correlation was confirmed in an independent cohort of human GBM. MIF overexpression has been reported in several cancer types, including GBM. We repurposed ibudilast, a specific MIF inhibitor, and treated patient derived cell lines. Ibudilast showed modest anti-proliferative activity however, when combined with TMZ, significant synergism was observed, resulting in cell cycle arrest and apoptosis. In vivo, combined ibudilast and TMZ treatment of a patient derived xenograft (PDX) model resulted in significantly longer overall survival. Our findings have significant clinical implications for people with GBM. Since clinical trials involving ibudilast have shown no adverse side effects and the drug readily penetrates the blood brain barrier, treatment of GBM with this combination is clinically achievable.