bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality
Authors: Carballo J. , Santos B. A. C. M. , Zappacosta D. , Garbus I. , Selva J. P. , Gallo C. A. , Díaz A. , Albertini E. , Caccamo M. , Echenique V. 
Published: July 2019

AbstractThe Poaceae constitute a taxon of flowering plants (grasses) that cover almost all Earth’s inhabitable range and comprises some of the genera most commonly used for human and animal nutrition. Many of these crops have been sequenced, like rice, Brachypodium, maize and, more recently, wheat. Some important members are still considered orphan crops, lacking a sequenced genome, but having important traits that make them attractive for sequencing. Among these traits is apomixis, clonal reproduction by seeds, present in some members of the Poaceae like Eragrostis curvula. A de novo, high-quality genome assembly and annotation for E. curvula have been obtained by sequencing 602 Mb of a diploid genotype using a strategy that combined long-read length sequencing with chromosome conformation capture. The scaffold N50 for this assembly was 43.41 Mb and the annotation yielded 56,469 genes. The availability of this genome assembly has allowed us to identify regions associated with forage quality and to develop strategies to sequence and assemble the complex tetraploid genotypes which harbor the apomixis control region(s). Understanding and subsequently manipulating the genetic drivers underlying apomixis could revolutionize agriculture.
Fingerprinting Proterozoic Bedrock in Interior Wilkes Land, East Antarctica
Authors: Maritati Alessandro , Halpin Jacqueline A. , Whittaker Joanne M. , Daczko Nathan R. 
Published: July 2019

AbstractWilkes Land in East Antarctica remains one of the last geological exploration frontiers on Earth. Hidden beneath kilometres of ice, its bedrock preserves a poorly-understood tectonic history that mirrors that of southern Australia and holds critical insights into past supercontinent cycles. Here, we use new and recently published Australian and Antarctic geological and geophysical data to present a novel interpretation of the age and character of crystalline basement and sedimentary cover of interior Wilkes Land. We combine new zircon U–Pb and Hf isotopic data from remote Antarctic outcrops with aeromagnetic data observations from the conjugate Australian-Antarctic margins to identify two new Antarctic Mesoproterozoic basement provinces corresponding to the continuation of the Coompana and Madura provinces of southern Australia into Wilkes Land. Using both detrital zircon U–Pb–Hf and authigenic monazite U–Th–Pb isotopic data from glacial erratic sandstone samples, we identify the presence of Neoproterozoic sedimentary rocks covering Mesoproterozoic basement. Together, these new geological insights into the ice-covered bedrock of Wilkes Land substantially improve correlations of Antarctic and Australian geological elements and provide key constraints on the tectonic architecture of this sector of the East Antarctic Shield and its role in supercontinent reconstructions.
Structural visualization of key steps in nucleosome reorganization by human FACT
Authors: Mayanagi Kouta , Saikusa Kazumi , Miyazaki Naoyuki , Akashi Satoko , Iwasaki Kenji , Nishimura Yoshifumi , Morikawa Kosuke , Tsunaka Yasuo 
Published: July 2019

AbstractFacilitates chromatin transcription (FACT) is a histone chaperone, which accomplishes both nucleosome assembly and disassembly. Our combined cryo-electron microscopy (EM) and native mass spectrometry (MS) studies revealed novel key steps of nucleosome reorganization conducted by a Mid domain and its adjacent acidic AID segment of human FACT. We determined three cryo-EM structures of respective octasomes complexed with the Mid-AID and AID regions, and a hexasome alone. We discovered extensive contacts between a FACT region and histones H2A, H2B, and H3, suggesting that FACT is competent to direct functional replacement of a nucleosomal DNA end by its phosphorylated AID segment (pAID). Mutational assays revealed that the aromatic and phosphorylated residues within pAID are essential for octasome binding. The EM structure of the hexasome, generated by the addition of Mid-pAID or pAID, indicated that the dissociation of H2A-H2B dimer causes significant alteration from the canonical path of the nucleosomal DNA.
Increase in weighting of vision vs. proprioception associated with force field adaptation
Authors: Sexton Brandon M. , Liu Yang , Block Hannah J. 
Published: July 2019

AbstractHand position can be estimated by vision and proprioception (position sense). The brain is thought to weight and integrate these percepts to form a multisensory estimate of hand position with which to guide movement. Force field adaptation, a type of cerebellum-dependent motor learning, is associated with both motor and proprioceptive changes. The cerebellum has connections with multisensory parietal regions; however, it is unknown if force adaptation is associated with changes in multisensory perception. If force adaptation affects all relevant sensory modalities similarly, the brain’s weighting of vision vs. proprioception should be maintained. Alternatively, if force perturbation is interpreted as somatosensory unreliability, vision may be up-weighted relative to proprioception. We assessed visuo-proprioceptive weighting with a perceptual estimation task before and after subjects performed straight-ahead reaches grasping a robotic manipulandum. Each subject performed one session with a clockwise or counter-clockwise velocity-dependent force field, and one session in a null field. Subjects increased their weight of vision vs. proprioception in the force field session relative to the null session, regardless of force field direction, in the straight-ahead dimension (F1,44 = 5.13, p = 0.029). This suggests that force field adaptation is associated with an increase in the brain’s weighting of vision vs. proprioception.
Strain-stress study of AlxGa1−xN/AlN heterostructures on c-plane sapphire and related optical properties
Authors: Feng Yining , Saravade Vishal , Chung Ting-Fung , Dong Yongqi , Zhou Hua , Kucukgok Bahadir , Ferguson Ian T. , Lu Na 
Published: July 2019

AbstractThis work presents a systematic study of stress and strain of AlxGa1−xN/AlN with composition ranging from GaN to AlN, grown on a c-plane sapphire by metal-organic chemical vapor deposition, using synchrotron radiation high-resolution X-ray diffraction and reciprocal space mapping. The c-plane of the AlxGa1−xN epitaxial layers exhibits compressive strain, while the a-plane exhibits tensile strain. The biaxial stress and strain are found to increase with increasing Al composition, although the lattice mismatch between the AlxGa1−xN and the buffer layer AlN gets smaller. A reduction in the lateral coherence lengths and an increase in the edge and screw dislocations are seen as the AlxGa1−xN composition is varied from GaN to AlN, exhibiting a clear dependence of the crystal properties of AlxGa1−xN on the Al content. The bandgap of the epitaxial layers is slightly lower than predicted value due to a larger tensile strain effect on the a-axis compared to the compressive strain on the c-axis. Raman characteristics of the AlxGa1−xN samples exhibit a shift in the phonon peaks with the Al composition. The effect of strain on the optical phonon energies of the epitaxial layers is also discussed.
Stable, predictable and training-free operation of superconducting Bi-2212 Rutherford cable racetrack coils at the wire current density of 1000 A/mm2
Authors: Shen Tengming , Bosque Ernesto , Davis Daniel , Jiang Jianyi , White Marvis , Zhang Kai , Higley Hugh , Turqueti Marcos , Huang Yibing , Miao Hanping , Trociewitz Ulf , Hellstrom Eric , Parrell Jeffrey , Hunt Andrew , Gourlay Stephen , Prestemon Soren , Larbalestier David 
Published: July 2019

AbstractHigh-temperature superconductors (HTS) could enable high-field magnets stronger than is possible with Nb-Ti and Nb3Sn, but two challenges have so far been the low engineering critical current density JE, especially in high-current cables, and the danger of quenches. Most HTS magnets made so far have been made out of REBCO coated conductor. Here we demonstrate stable, reliable and training-quench-free performance of Bi-2212 racetrack coils wound with a Rutherford cable fabricated from wires made with a new precursor powder. These round multifilamentary wires exhibited a record JE up to 950 A/mm2 at 30 T at 4.2 K. These coils carried up to 8.6 kA while generating 3.5 T at 4.2 K at a JE of 1020 A/mm2. Different from the unpredictable training performance of Nb-Ti and Nb3Sn magnets, these Bi-2212 magnets showed no training quenches and entered the flux flow state in a stable manner before thermal runaway and quench occurred. Also different from Nb-Ti, Nb3Sn, and REBCO magnets for which localized thermal runaways occur at unpredictable locations, the quenches of Bi-2212 magnets consistently occurred in the high field regions over a long conductor length. These characteristics make quench detection simple, enabling safe protection, and suggest a new paradigm of constructing quench-predictable superconducting magnets from Bi-2212.
Integrated targeted metabolomic and lipidomic analysis: A novel approach to classifying early cystic precursors to invasive pancreatic cancer
Authors: Gaiser Rogier Aäron , Pessia Alberto , Ateeb Zeeshan , Davanian Haleh , Fernández Moro Carlos , Alkharaan Hassan , Healy Katie , Ghazi Sam , Arnelo Urban , Valente Roberto , Velagapudi Vidya , Sällberg Chen Margaret , Del Chiaro Marco 
Published: July 2019

AbstractPancreatic cystic neoplasms (PCNs) are a highly prevalent disease of the pancreas. Among PCNs, Intraductal Papillary Mucinous Neoplasms (IPMNs) are common lesions that may progress from low-grade dysplasia (LGD) through high-grade dysplasia (HGD) to invasive cancer. Accurate discrimination of IPMN-associated neoplastic grade is an unmet clinical need. Targeted (semi)quantitative analysis of 100 metabolites and >1000 lipid species were performed on peri-operative pancreatic cyst fluid and pre-operative plasma from IPMN and serous cystic neoplasm (SCN) patients in a pancreas resection cohort (n = 35). Profiles were correlated against histological diagnosis and clinical parameters after correction for confounding factors. Integrated data modeling was used for group classification and selection of the best explanatory molecules. Over 1000 different compounds were identified in plasma and cyst fluid. IPMN profiles showed significant lipid pathway alterations compared to SCN. Integrated data modeling discriminated between IPMN and SCN with 100% accuracy and distinguished IPMN LGD or IPMN HGD and invasive cancer with up to 90.06% accuracy. Free fatty acids, ceramides, and triacylglycerol classes in plasma correlated with circulating levels of CA19-9, albumin and bilirubin. Integrated metabolomic and lipidomic analysis of plasma or cyst fluid can improve discrimination of IPMN from SCN and within PMNs predict the grade of dysplasia.
TNFAIP3 genetic polymorphisms reduce ankylosing spondylitis risk in Eastern Chinese Han population
Authors: Yang Jiajia , Hu Xingxing , Wu Meng , Ma Yubo , Zhang Xu , Chen Mengya , Yuan Yaping , Han Renfang , Liu Rui , Guan Shiyang , Deng Jixiang , Xu Shanshan , Gao Xing , Xu Shengqian , Shuai Zongwen , Jiang Shanqun , Guan Shihe , Chen Liwen , Pan Faming 
Published: July 2019

AbstractThis study was conducted to clarify the associations of tumor necrosis factor-α induced protein 3 (TNFAIP3) and TNFAIP3-interacting protein 1 (TNIP1) genetic polymorphisms with ankylosing spondylitis (AS) susceptibility. Five single nucleotide polymorphisms (SNPs) in TNFAIP3 gene and four in TNIP1 gene were genotyped in 667 AS patients and 667 matched healthy controls. Genotypes and haplotype analysis were conducted by using SPSS 23.0 and Haploview 4.2 software. The T allele and CT genotype in TNFAIP3 rs10499194 were significantly associated with a reduced AS risk (T allele vs. C allele, OR = 0.619, 95% CI = 0.430–0.889, P = 0.009; CT vs. CC, OR = 0.603, 95% CI = 0.416–0.875, P = 0.007). However, no association remained significant after Bonferroni correction. The rs13207033A- rs10499194T haplotype of TNFAIP3 conferred a protective effect on AS susceptibility. Stratification analyses suggested that rs10499194 polymorphism decreased the risk of AS in the male subgroup, subgroup aged ≥ 29, HLA-B27 positive subgroup as well as the subgroups of BASFI < 4 and BASDAI < 4 (all P < 0.05). Furthermore, the functional annotation suggested a potential function of rs10499194 mutation. Our results demonstrated that TNFAIP3 rs10499194 polymorphism may be associated with a reduced risk of AS.
REV-ERBα and REV-ERBβ function as key factors regulating Mammalian Circadian Output
Authors: Ikeda Ryosuke , Tsuchiya Yoshiki , Koike Nobuya , Umemura Yasuhiro , Inokawa Hitoshi , Ono Ryutaro , Inoue Maho , Sasawaki Yuh , Grieten Tess , Okubo Naoki , Ikoma Kazuya , Fujiwara Hiroyoshi , Kubo Toshikazu , Yagita Kazuhiro 
Published: July 2019

AbstractThe circadian clock regulates behavioural and physiological processes in a 24-h cycle. The nuclear receptors REV-ERBα and REV-ERBβ are involved in the cell-autonomous circadian transcriptional/translational feedback loops as transcriptional repressors. A number of studies have also demonstrated a pivotal role of REV-ERBs in regulation of metabolic, neuronal, and inflammatory functions including bile acid metabolism, lipid metabolism, and production of inflammatory cytokines. Given the multifunctional role of REV-ERBs, it is important to elucidate the mechanism through which REV-ERBs exert their functions. To this end, we established a Rev-erbα/Rev-erbβ double-knockout mouse embryonic stem (ES) cell model and analyzed the circadian clock and clock-controlled output gene expressions. A comprehensive mRNA-seq analysis revealed that the double knockout of both Rev-erbα and Rev-erbβ does not abrogate expression rhythms of E-box-regulated core clock genes but drastically changes a diverse set of other rhythmically-expressed output genes. Of note, REV-ERBα/β deficiency does not compromise circadian expression rhythms of PER2, while REV-ERB target genes, Bmal1 and Npas2, are significantly upregulated. This study highlight the relevance of REV-ERBs as pivotal output mediators of the mammalian circadian clock.
The transcriptome of potato tuber phellogen reveals cellular functions of cork cambium and genes involved in periderm formation and maturation
Authors: Vulavala Vijaya K. R. , Fogelman Edna , Faigenboim Adi , Shoseyov Oded , Ginzberg Idit 
Published: July 2019

AbstractThe periderm is a protective corky tissue that is formed through the cambial activity of phellogen cells, when the outer epidermis is damaged. Timely periderm formation is critical to prevent pathogen invasion and water loss. The outer layers of the potato periderm, the tuber skin, serves as a model to study cork development. Early in tuber development the phellogen becomes active and produces the skin. During tuber maturation it becomes inactive and the skin adheres to the tuber flesh. The characterization of potato phellogen may contribute to the management of costly agricultural problems related to incomplete skin-set and the resulting skinning injuries, and provide us with new knowledge regarding cork development in planta. A transcriptome of potato tuber phellogen isolated by laser capture microdissection indicated similarity to vascular cambium and the cork from trees. Highly expressed genes and transcription factors indicated that phellogen activation involves cytokinesis and gene reprograming for the establishment of a dedifferentiation state; whereas inactivation is characterized by activity of genes that direct organ identity in meristem and cell-wall modifications. The expression of selected genes was analyzed using qPCR in native and wound periderm at distinct developmental stages. This allowed the identification of genes involved in periderm formation and maturation.
Establishing next-generation pest control services in rice fields: eco-agriculture
Authors: Ali M. P. , Bari M. N. , Haque S. S. , Kabir M. M. M. , Afrin S. , Nowrin F. , Islam M. S. , Landis D. A. 
Published: July 2019

AbstractPesticides are commonly used in food crop production systems to control crop pests and diseases and ensure maximum yield with high market value. However, the accumulation of these chemical inputs in crop fields increases risks to biodiversity and human health. In addition, people are increasingly seeking foods in which pesticide residues are low or absent and that have been produced in a sustainable fashion. More than half of the world’s human population is dependent on rice as a staple food and chemical pesticides to control pests is the dominant paradigm in rice production. In contrast, the use of natural enemies to suppress crop pests has the potential to reduce chemical pesticide inputs in rice production systems. Currently, predators and parasitoids often do not persist in rice production landscapes due to the absence of shelter or nutritional sources. In this study, we modified the existing rice landscape through an eco-engineering technique that aims to increase natural biocontrol agents for crop protection. In this system, planting nectar-rich flowering plants on rice bunds provides food and shelter to enhance biocontrol agent activity and reduce pest numbers, while maintaining grain yield. The abundance of predators and parasitoids and parasitism rates increased significantly in the eco-engineering plots compared to the insecticide-treated and control plots. Moreover, a significantly lower number of principal insect pests and damage symptoms were found in treatments where flowering plants were grown on bunds than in plots where such plants were not grown. This study indicates that manipulating habitat for natural enemies in rice landscapes enhances pest suppression and maintains equal yields while reducing the need for insecticide use in crop fields.
Dual resistance of transgenic plants against Cymbidium mosaic virus and Odontoglossum ringspot virus
Authors: Chen Ting-Yu , Pai Hsuan , Hou Liang-Yu , Lee Shu-Chuan , Lin Tzu-Tung , Chang Chih-Hao , Hsu Fu-Chen , Hsu Yau-Heiu , Lin Na-Sheng 
Published: July 2019

AbstractTaxonomically distinctCymbidium mosaic potexvirus(CymMV) andOdontoglossum ringspot tobamovirus(ORSV) are two of the most prevalent viruses worldwide; when co-infecting orchids, they cause synergistic symptoms. Because of the huge economic loss in quality and quantity in the orchid industry with virus-infected orchids, virus-resistant orchids are urgently needed. To date, no transgenic resistant lines against these two viruses have been reported. In this study, we generated transgenicNicotiana benthamianaexpressing various constructs of partial CymMV and ORSV genomes. Several transgenic lines grew normally and remained symptomless after mixed inoculation with CymMV and ORSV. The replication of CymMV and ORSV was approximately 70–90% lower in protoplasts of transgenic lines than wild-type (WT) plants. Of note, we detected extremely low or no viral RNA or capsid protein of CymMV and ORSV in systemic leaves of transgenic lines after co-infection. Grafting experiments further revealed that CymMV and ORSV trafficked extremely inefficiently from co-infected WT stocks to transgenic scions, presumably due to RNA-mediated interference. This study reports the first successful creation of dual resistant transgenic lines against CymMV and ORSV. Our studies shed light on the commercial development of transgenic orchid production to combat the global viral threat.
Hemodynamic Performance of Multilayer Stents in the Treatment of Aneurysms with a Branch Attached
Authors: Li Zhongyou , Hu Lijuan , Chen Chong , Wang Zhenze , Zhou Zhihong , Chen Yu 
Published: July 2019

AbstractAlthough multilayer stents (MSs) can be used to treat aneurysm effectively, for some aneurysms with branches attached, the hemodynamic mechanisms are still unclear. In this work, we modeled five cases that involve 1–4-layer stents implanted in aneurysms with side branches, and the numerical approach was used. Case 1 corresponds to an aneurysm without a stent, and cases 2–5 represent 1–4-layer stents being employed within aneurysms, respectively. The results showed that the velocity within the sac declined dramatically and the eddies’ intensity weakened with increased number of stent layers, time-averaged wall shear stress (TAWSS), and nitric oxide production rate (TARNO) dropped linearly with increase in stent porosity, and oscillatory shear index (OSI) and relative residence time (RRT) increased evidently with MS intervention. Moreover, the MSs had a slight effect on the patency of the side branch; its flow rate was still above the normal case than without aneurysm. It can be concluded that MSs are helpful in promoting the growth of thrombus within the aneurysm through an isolated hemodynamic environment and keeping the branch unobstructed, but more clinical evidences are required.
Enhancement of trapping efficiency by utilizing a hollow sinh-Gaussian beam
Authors: Liu Zhirong , Wang Xun , Hang Kelin 
Published: July 2019

AbstractPropagation properties and optical forces upon a Rayleigh dielectric sphere for a newly proposed hollow sinh-Gaussian beam (HsGB) are intensively investigated. In view of the targeted laser beam’s unique tight focusing properties that a significantly sharp, peak-centered, and adjustable intensity distribution would be produced in the focal vicinity, the tightly focused HsGB could be exploited to trap and manipulate nano-sized dielectric spheres with high-refractive index in the focal region. The interesting and meaningful features for the novel HsGB mainly include that, compared with the conventional fundamental Gaussian beams under the same optical power, the tightly focused HsGB has much higher intensity gradient and deeper potential well through optimizing targeted laser beam’s parameters. Theretofore, the novel HsGB optical tweezers could drastically enhance its trapping efficiency. Finally, the trapping stability conditions are discussed in detail. The analytical and numerical results obtained here could provide a directive suggestion for researchers in optimizing experimental parameters in constructing a novel HsGB tweezers and making use of a HsGB.