bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species
Authors: Yi Xian-Gui , Yu Xia-Qing , Chen Jie , Zhang Min , Liu Shao-Wei , Zhu Hong , Li Meng , Duan Yi-Fan , Chen Lin , Wu Lei , Zhu Shun , Sun Zhong-Shuai , Liu Xin-Hong , Wang Xian-Rong 
Published: October 2020

AbstractCerasus serrulatais a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly ofC. serrulataby the use of Nanopore and Hi-C sequencing technologies. The assembledC. serrulatagenome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated thatC. serrulataandC. aviumhave 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 ofC. serrulataare distributed on all chromosomes ofC. avium, implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed thatC. serrulatahas 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The presentC. serrulataspecies diverged fromPrunus yedoensis~17.34 million years ago (Mya), while the divergence ofC. serrulataandC. aviumwas estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified inC. serrulata, accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies inC. serrulata, respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searchingC. serrulatawithin the PRGdb. This research provides high-quality genomic information aboutC. serrulataas well as insights into the evolutionary history ofCerasusspecies.
PpINH1, an invertase inhibitor, interacts with vacuolar invertase PpVIN2 in regulating the chilling tolerance of peach fruit
Authors: Wang Xingxing , Chen Yi , Jiang Shu , Xu Feng , Wang Hongfei , Wei Yingying , Shao Xingfeng 
Published: October 2020

AbstractSucrose metabolism, particularly the decomposition of sucrose by invertase, plays a central role in plant responses to cold stress. Invertase inhibitors (INHs) evolved in higher plants as essential regulators of sucrose metabolism. By limiting invertase activity, INHs keep cellular sugar levels elevated, which provides enhanced protection to plants under stress. Our results showed that the expression of PpVIN2, the only vacuolar invertase (VIN) gene in peach fruit sensitive to chilling temperatures, increases significantly during cold storage, while VIN enzyme activity increases more modestly. We also found that peach fruit transiently overexpressing PpINH1 had decreased VIN activity. Interactions of PpINH1 and PpVIN2 with recombinant proteins were shown by yeast two-hybrid assays and bimolecular fluorescence complementation assays, as well as in vitro. During cold storage, trehalose-treated peach fruit had significantly increased PpINH1 expression, decreased VIN enzyme activity, and significantly higher sucrose content than did untreated fruit. As a result, the treated fruit had enhanced resistance to chilling injury. Collectively, our data show that the post-translational repression of VIN enzyme activity by PpINH1 helps maintain sucrose levels in peach fruit during cold storage, thereby improving resistance to chilling injury.
Self-compatibility in peach [Prunus persica (L.) Batsch]: patterns of diversity surrounding the S-locus and analysis of SFB alleles
Authors: Abdallah Donia , Baraket Ghada , Perez Veronica , Salhi Hannachi Amel , Hormaza Jose I. 
Published: October 2020

AbstractSelf-incompatibility (SI) to self-compatibility (SC) transition is one of the most frequent and prevalent evolutionary shifts in flowering plants. Prunus L. (Rosaceae) is a genus of over 200 species most of which exhibit a Gametophytic SI system. Peach [Prunus persica (L.) Batsch; 2n = 16] is one of the few exceptions in the genus known to be a fully self-compatible species. However, the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and, in order to fill that gap, in this study 24 peach accessions were analyzed. Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes. The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant (P > 0.05), except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus. Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additional α-helices at the C-termini. Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2, while the SFB1 seemed to evolve neutrally. Thus, our results show that the SFB2 allele diversified after P. persica and P. dulcis (almond) divergence, a period which is characterized by an important bottleneck, while SFB1 diversified at a transition time between the bottleneck and population expansion.
Mechanism of self/nonself-discrimination in Brassica self-incompatibility
Authors: Murase Kohji , Moriwaki Yoshitaka , Mori Tomoyuki , Liu Xiao , Masaka Chiho , Takada Yoshinobu , Maesaki Ryoko , Mishima Masaki , Fujii Sota , Hirano Yoshinori , Kawabe Zen , Nagata Koji , Terada Tohru , Suzuki Go , Watanabe Masao , Shimizu Kentaro , Hakoshima Toshio , Takayama Seiji 
Published: October 2020

AbstractSelf-incompatibility (SI) is a breeding system that promotes cross-fertilization. In Brassica, pollen rejection is induced by a haplotype-specific interaction between pistil determinant SRK (S receptor kinase) and pollen determinant SP11 (S-locus Protein 11, also named SCR) from the S-locus. Although the structure of the B. rapa S9-SRK ectodomain (eSRK) and S9-SP11 complex has been determined, it remains unclear how SRK discriminates self- and nonself-SP11. Here, we uncover the detailed mechanism of self/nonself-discrimination in Brassica SI by determining the S8-eSRK–S8-SP11 crystal structure and performing molecular dynamics (MD) simulations. Comprehensive binding analysis of eSRK and SP11 structures reveals that the binding free energies are most stable for cognate eSRK–SP11 combinations. Residue-based contribution analysis suggests that the modes of eSRK–SP11 interactions differ between intra- and inter-subgroup (a group of phylogenetically neighboring haplotypes) combinations. Our data establish a model of self/nonself-discrimination in Brassica SI.
Strong enhancement of magnetic order from bulk to stretched monolayer FeSe as Hund’s metals
Authors: Moon Chang-Youn 
Published: October 2020

AbstractDespite of the importance of magnetism in possible relation to other key properties in iron-based superconductors, its understanding is still far from complete especially for FeSe systems. On one hand, the origin of the absence of magnetic orders in bulk FeSe is yet to be clarified. On the other hand, it is still not clear how close monolayer FeSe on SrTiO3, with the highest transition temperature among iron-based superconductors, is to a magnetic instability. Here we investigate magnetic properties of bulk and monolayer FeSe using dynamical mean-field theory combined with density-functional theory. We find that suppressed magnetic order in bulk FeSe is associated with the reduction of interorbital charge fluctuations, an effect of Hund’s coupling, enhanced by a larger crystal-field splitting. Meanwhile, spatial isolation of Fe atoms in expanded monolayer FeSe leads into a strong magnetic order, which is completely destroyed by a small electron doping. Our work provides a comprehensive understanding of the magnetic order in iron-based superconductors and other general multi-orbital correlated systems as Hund’s metals.
Surface Josephson plasma waves in a high-temperature superconductor
Authors: Lu Qianbo , Bollinger Anthony T. , He Xi , Sundling Robert , Bozovic Ivan , Gozar Adrian 
Published: October 2020

AbstractElectron density oscillations with acoustic dispersions and sustained at boundaries between different media provide information about surface and interface properties of heterostructures. In ultrathin metallic films these plasmonic excitations are heavily damped. Superconductivity is predicted to reduce dissipation allowing detection of these resonances. Emerging low-loss interface Cooper-pair waves have been studied before, however, the observation of surface-confined Josephson plasmons in highly anisotropic superconductors has remained elusive. Here, we report on generation and coupling to these excitations in an ultrathin single-crystal film of high-temperature superconductor La1.85Sr0.15CuO4. The film becomes brighter than Au below the critical temperature when probed with sub-gap THz photons. We show that the enhanced signal in the superconducting state, which can be visualized with a spatial resolution better than λ/3000, originates from near-field coupling of light to surface Josephson plasmons. Our results open a path towards non-invasive investigation of enhanced superconductivity in artificial multilayers, buried interface states in topological heterostructures, and non-linear phenomena in Josephson devices.
Transcriptional modulation of AREB-1 by CRISPRa improves plant physiological performance under severe water deficit
Authors: de Melo Bruno Paes , Lourenço-Tessutti Isabela Tristan , Paixão Joaquin Felipe Roca , Noriega Daniel David , Silva Maria Cristina Mattar , de Almeida-Engler Janice , Fontes Elizabeth Pacheco Batista , Grossi-de-Sa Maria Fatima 
Published: October 2020

AbstractPlants are sessile organisms, which are vulnerable to environmental stresses. As such, plants have developed multiple molecular, physiological, and cellular mechanisms to cope with natural stressors. However, these environmental adversities, including drought, are sources of the main agribusiness problems since they interfere with plant growth and productivity. Particularly under water deprivation conditions, the abscisic acid-responsive element-binding protein AREB1/ABF2 plays an important role in drought stress response and physiological adaptation. In this investigation, we provide substantial confirmation for the role of AREB1/ABF2 in plant survival under severe water deficit using the CRISPR activation (CRISPRa) technique to enhance the AREB1 gene expression. In our strategy, the inactive nuclease dCas9 was fused with an Arabidopsis histone acetyltransferase 1, which improves gene expression by remodeling chromatin. The AREB1 overexpression promotes an improvement in the physiological performance of the transgenic homozygous plants under drought, which was associated with an increase in chlorophyll content, antioxidant enzyme activity, and soluble sugar accumulation, leading to lower reactive oxygen species accumulation. Finally, we found that the CRISPR-mediated up-regulation of AREB1 changes the abundance of several downstream ABA-inducible genes, allowing us to report that CRISPRa dCas9-HAT is a valuable biotechnological tool to improve drought stress tolerance through the positive regulation of AREB1.
RETRACTED ARTICLE: Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family
Authors: Sarkar Indrani , Dey Prateek , Sharma Sanjeev Kumar , Ray Swapna Devi , Kochiganti Venkata Hanumat Sastry , Singh Renu , Pramod Padmanabhan , Singh Ram Pratap 
Published: October 2020

AbstractMitochondrial genome provides useful information about species concerning its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,672 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with two rRNAs and 22 tRNAs were detected. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Duplicated control regions were found in the newly sequenced mitogenome. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over thirteen protein-coding genes in yellow-billed babbler mitogenome. Ka/Ks analysis indicated the highest synonymous substitution rate in the nad6 gene. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogeny results placed T. affinis in a separate group, a sister group of Garrulax. Overall, our results provide a useful information for future studies on the evolutionary and adaptive mechanisms of birds belong to the Leiothrichidae family.
A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents
Authors: Deichler Alfonso , Carrasco Denisse , Lopez-Jury Luciana , Vega-Zuniga Tomas , Márquez Natalia , Mpodozis Jorge , Marín Gonzalo J. 
Published: October 2020

AbstractThe parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors.
Thermal neutron transmutation doping of GaN semiconductors
Authors: Barber R. , Nguyen Q. , Brockman J. , Gahl J. , Kwon J. 
Published: October 2020

AbstractHigh quality Ge doping of GaN is demonstrated using primarily thermal neutrons for the first time. In this study, GaN was doped with Ge to concentrations from 1016 Ge atoms/cm3 to 1018 Ge atoms/cm3. The doping concentrations were measured using gamma-ray spectroscopy and confirmed using SIMS analysis. The data from SIMS analysis also show consistent Ge doping concentration throughout the depth of the GaN wafers. After irradiation, the GaN was annealed in a nitrogen environment at 950 °C for 30 min. The neutron doping process turns out to produce spatially uniform doping throughout the whole volume of the GaN substrate.
Radionecrosis and cellular changes in small volume stereotactic brain radiosurgery in a porcine model
Authors: Zaer Hamed , Glud Andreas Nørgaard , Schneider Bret M. , Lukacova Slávka , Vang Hansen Kim , Adler John R. , Høyer Morten , Jensen Morten Bjørn , Hansen Rune , Hoffmann Lone , Worm Esben Schjødt , Sørensen Jens Chr. Hedemann , Orlowski Dariusz 
Published: October 2020

AbstractStereotactic radiosurgery (SRS) has proven an effective tool for the treatment of brain tumors, arteriovenous malformation, and functional conditions. However, radiation-induced therapeutic effect in viable cells in functional SRS is also suggested. Evaluation of the proposed modulatory effect of irradiation on neuronal activity without causing cellular death requires the knowledge of radiation dose tolerance at very small tissue volume. Therefore, we aimed to establish a porcine model to study the effects of ultra-high radiosurgical doses in small volumes of the brain. Five minipigs received focal stereotactic radiosurgery with single large doses of 40–100 Gy to 5–7.5 mm fields in the left primary motor cortex and the right subcortical white matter, and one animal remained as unirradiated control. The animals were followed-up with serial MRI,
PET scans, and histology 6 months post-radiation. We observed a dose-dependent relation of the histological and MRI changes at 6 months post-radiation. The necrotic lesions were seen in the grey matter at 100 Gy and in white matter at 60 Gy. Furthermore, small volume radiosurgery at different dose levels induced vascular, as well as neuronal cell changes and glial cell remodeling.
Short-term variability of the human serum metabolome depending on nutritional and metabolic health status
Authors: Agueusop Inoncent , Musholt Petra B. , Klaus Beate , Hightower Kendra , Kannt Aimo 
Published: October 2020

AbstractThe intra-individual variability of the human serum metabolome over a period of 4 weeks and its dependence on metabolic health and nutritional status was investigated in a single-center study under tightly controlled conditions in healthy controls, pre-diabetic individuals and patients with type-2 diabetes mellitus (T2DM, n = 10 each). Untargeted metabolomics in serum samples taken at three different days after overnight fasts and following intake of a standardized mixed meal showed that the human serum metabolome is remarkably stable: The median intra-class correlation coefficient (ICC) across all metabolites and all study participants was determined as 0.65. ICCs were similar for the three different health groups, before and after meal intake, and for different metabolic pathways. Only 147 out of 1438 metabolites (10%) had an ICC below 0.4 indicating poor stability over time. In addition, we confirmed previously identified metabolic signatures differentiating healthy, pre-diabetic and diabetic individuals. To our knowledge, this is the most comprehensive study investigating the temporal variability of the human serum metabolome under such tightly controlled conditions.
Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases
Authors: Park Ji In , Kim Tae-Yoon , Oh Bumjo , Cho Hyunjeong , Kim Ji Eun , Yoo Seong Ho , Lee Jung Pyo , Kim Yon Su , Chun Jongsik , Kim Bong-Soo , Lee Hajeong 
Published: October 2020

AbstractImmunoglobulin A nephropathy (IgAN) involves repeated events of gross haematuria with concurrent upper airway infections. The mucosal immune system, especially the tonsil, is considered the initial site of inflammation, although the role of the tonsillar microbiota has not been established in IgAN. In this study, we compared the tonsillar microbiota of patients with IgAN (n = 21) and other glomerular diseases (n = 36) as well as, healthy controls (n = 23) from three medical centres in Korea. The microbiota was analysed from tonsil swabs using the Illumina MiSeq system based on 16S rRNA gene. Tonsillar bacterial diversity was higher in IgAN than in other glomerular diseases, although it did not differ from that of healthy controls. Principal coordinates analysis revealed differences between the tonsillar microbiota of IgAN and both healthy and disease controls. The proportions of Rahnella, Ruminococcus_g2, and Clostridium_g21 were significantly higher in patients with IgAN than in healthy controls (corrected p < 0.05). The relative abundances of several taxa were correlated with the estimated glomerular filtration rate, blood urea nitrogen, haemoglobin, and serum albumin levels. Based on our findings, tonsillar microbiota may be associated with clinical features and possible immunologic pathogenesis of IgAN.
Measurement of the tilt of a moving domain wall shows precession-free dynamics in compensated ferrimagnets
Authors: Haltz E. , Sampaio J. , Krishnia S. , Berges L. , Weil R. , Mougin A. 
Published: October 2020

AbstractOne fundamental obstacle to efficient ferromagnetic spintronics is magnetic precession, which intrinsically limits the dynamics of magnetic textures. We experimentally demonstrate that this precession vanishes when the net angular momentum is compensated in domain walls driven by spin–orbit torque in a ferrimagnetic GdFeCo/Pt track. We use transverse in-plane fields to provide a robust and parameter-free measurement of the domain wall internal magnetisation angle, demonstrating that, at the angular compensation, the DW tilt is zero, and thus the magnetic precession that caused it is suppressed. Our results highlight the mechanism of faster and more efficient dynamics in materials with multiple spin lattices and vanishing net angular momentum, promising for high-speed, low-power spintronic applications.
Exploring food contents in scientific literature with FoodMine
Authors: Hooton Forrest , Menichetti Giulia , Barabási Albert-László 
Published: October 2020

AbstractThanks to the many chemical and nutritional components it carries, diet critically affects human health. However, the currently available comprehensive databases on food composition cover only a tiny fraction of the total number of chemicals present in our food, focusing on the nutritional components essential for our health. Indeed, thousands of other molecules, many of which have well documented health implications, remain untracked. To explore the body of knowledge available on food composition, we built FoodMine, an algorithm that uses natural language processing to identify papers from PubMed that potentially report on the chemical composition of garlic and cocoa. After extracting from each paper information on the reported quantities of chemicals, we find that the scientific literature carries extensive information on the detailed chemical components of food that is currently not integrated in databases. Finally, we use unsupervised machine learning to create chemical embeddings, finding that the chemicals identified by FoodMine tend to have direct health relevance, reflecting the scientific community’s focus on health-related chemicals in our food.