bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant
Authors: Wei Qingzhen , Wang Jinglei , Wang Wuhong , Hu Tianhua , Hu Haijiao , Bao Chonglai 
Published: September 2020

AbstractEggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. melongena-HQ) using a combination of Illumina, Nanopore and 10X genomics sequencing technologies and Hi-C technology for genome assembly. The assembled genome has a total size of ~1.17 Gb and 12 chromosomes, with a contig N50 of 5.26 Mb, consisting of 36,582 protein-coding genes. Repetitive sequences comprise 70.09% (811.14 Mb) of the eggplant genome, most of which are long terminal repeat (LTR) retrotransposons (65.80%), followed by long interspersed nuclear elements (LINEs, 1.54%) and DNA transposons (0.85%). The S. melongena-HQ eggplant genome carries a total of 563 accession-specific gene families containing 1009 genes. In total, 73 expanded gene families (892 genes) and 34 contraction gene families (114 genes) were functionally annotated. Comparative analysis of different eggplant genomes identified three types of variations, including single-nucleotide polymorphisms (SNPs), insertions/deletions (indels) and structural variants (SVs). Asymmetric SV accumulation was found in potential regulatory regions of protein-coding genes among the different eggplant genomes. Furthermore, we performed QTL-seq for eggplant fruit length using the S. melongena-HQ reference genome and detected a QTL interval of 71.29–78.26 Mb on chromosome E03. The gene Smechr0301963, which belongs to the SUN gene family, is predicted to be a key candidate gene for eggplant fruit length regulation. Moreover, we anchored a total of 210 linkage markers associated with 71 traits to the eggplant chromosomes and finally obtained 26 QTL hotspots. The eggplant HQ-1315 genome assembly can be accessed at http://eggplant-hq.cn. In conclusion, the eggplant genome presented herein provides a global view of genomic divergence at the whole-genome level and powerful tools for the identification of candidate genes for important traits in eggplant.
Mapping cellular-scale internal mechanics in 3D tissues with thermally responsive hydrogel probes
Authors: Mok Stephanie , Al Habyan Sara , Ledoux Charles , Lee Wontae , MacDonald Katherine N. , McCaffrey Luke , Moraes Christopher 
Published: September 2020

AbstractLocal tissue mechanics play a critical role in cell function, but measuring these properties at cellular length scales in living 3D tissues can present considerable challenges. Here we present thermoresponsive, smart material microgels that can be dispersed or injected into tissues and optically assayed to measure residual tissue elasticity after creep over several weeks. We first develop and characterize the sensors, and demonstrate that internal mechanical profiles of live multicellular spheroids can be mapped at high resolutions to reveal broad ranges of rigidity within the tissues, which vary with subtle differences in spheroid aggregation method. We then show that small sites of unexpectedly high rigidity develop in invasive breast cancer spheroids, and in an in vivo mouse model of breast cancer progression. These focal sites of increased intratumoral rigidity suggest new possibilities for how early mechanical cues that drive cancer cells towards invasion might arise within the evolving tumor microenvironment.
Role of higher-order exchange interactions for skyrmion stability
Authors: Paul Souvik , Haldar Soumyajyoti , von Malottki Stephan , Heinze Stefan 
Published: September 2020

AbstractTransition-metal interfaces and multilayers are a promising class of systems to realize nanometer-sized, stable magnetic skyrmions for future spintronic devices. For room temperature applications, it is crucial to understand the interactions which control the stability of isolated skyrmions. Typically, skyrmion properties are explained by the interplay of pair-wise exchange interactions, the Dzyaloshinskii-Moriya interaction and the magnetocrystalline anisotropy energy. Here, we demonstrate that higher-order exchange interactions – which have so far been neglected – can play a key role for the stability of skyrmions. We use an atomistic spin model parametrized from first-principles and compare three different ultrathin film systems. We consider all fourth-order exchange interactions and show that, in particular, the four-site four spin interaction has a large effect on the energy barrier preventing skyrmion and antiskyrmion collapse into the ferromagnetic state. Our work opens perspectives to stabilize topological spin structures even in the absence of Dzyaloshinskii-Moriya interaction.
A predictable conserved DNA base composition signature defines human core DNA replication origins
Authors: Akerman Ildem , Kasaai Bahar , Bazarova Alina , Sang Pau Biak , Peiffer Isabelle , Artufel Marie , Derelle Romain , Smith Gabrielle , Rodriguez-Martinez Marta , Romano Manuela , Kinet Sandrina , Tino Peter , Theillet Charles , Taylor Naomi , Ballester Benoit , Méchali Marcel 
Published: September 2020

AbstractDNA replication initiates from multiple genomic locations called replication origins. In metazoa, DNA sequence elements involved in origin specification remain elusive. Here, we examine pluripotent, primary, differentiating, and immortalized human cells, and demonstrate that a class of origins, termed core origins, is shared by different cell types and host ~80% of all DNA replication initiation events in any cell population. We detect a shared G-rich DNA sequence signature that coincides with most core origins in both human and mouse genomes. Transcription and G-rich elements can independently associate with replication origin activity. Computational algorithms show that core origins can be predicted, based solely on DNA sequence patterns but not on consensus motifs. Our results demonstrate that, despite an attributed stochasticity, core origins are chosen from a limited pool of genomic regions. Immortalization through oncogenic gene expression, but not normal cellular differentiation, results in increased stochastic firing from heterochromatin and decreased origin density at TAD borders.
Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication
Authors: Dutta Prasun , Talenti Andrea , Young Rachel , Jayaraman Siddharth , Callaby Rebecca , Jadhav Santosh Kumar , Dhanikachalam Velu , Manikandan Mayakannan , Biswa Bhim B. , Low Wai Y. , Williams John L. , Cook Elizabeth , Toye Phil , Wall Eileen , Djikeng Appolinaire , Marshall Karen , Archibald Alan L. , Gokhale Suresh , Kumar Satish , Hume David A. , Prendergast James G. D. 
Published: September 2020

AbstractMore people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.
Brain stimulation in zero gravity: transcranial magnetic stimulation (TMS) motor threshold decreases during zero gravity induced by parabolic flight
Authors: Badran Bashar W. , Caulfield Kevin A. , Cox Claire , Lopez James W. , Borckardt Jeffrey J. , DeVries William H. , Summers Philipp , Kerns Suzanne , Hanlon Colleen A. , McTeague Lisa M. , George Mark S. , Roberts Donna R. 
Published: September 2020

AbstractWe are just beginning to understand how spaceflight may impact brain function. As NASA proceeds with plans to send astronauts to the Moon and commercial space travel interest increases, it is critical to understand how the human brain and peripheral nervous system respond to zero gravity. Here, we developed and refined head-worn transcranial magnetic stimulation (TMS) systems capable of reliably and quickly determining the amount of electromagnetism each individual needs to detect electromyographic (EMG) threshold levels in the thumb (called the resting motor threshold (rMT)). We then collected rMTs in 10 healthy adult participants in the laboratory at baseline, and subsequently at three time points onboard an airplane: (T1) pre-flight at Earth gravity, (T2) during zero gravity periods induced by parabolic flight and (T3) post-flight at Earth gravity. Overall, the subjects required 12.6% less electromagnetism applied to the brain to cause thumb muscle activation during weightlessness compared to Earth gravity, suggesting neurophysiological changes occur during brief periods of zero gravity. We discuss several candidate explanations for this finding, including upward shift of the brain within the skull, acute increases in cortical excitability, changes in intracranial pressure, and diffuse spinal or neuromuscular system effects. All of these possible explanations warrant further study. In summary, we documented neurophysiological changes during brief episodes of zero gravity and thus highlighting the need for further studies of human brain function in altered gravity conditions to optimally prepare for prolonged microgravity exposure during spaceflight.
Dual similarity solutions of MHD stagnation point flow of Casson fluid with effect of thermal radiation and viscous dissipation: stability analysis
Authors: Lund Liaquat Ali , Omar Zurni , Khan Ilyas , Baleanu Dumitru , Nisar Kottakkaran Sooppy 
Published: September 2020

AbstractIn this paper, the rate of heat transfer of the steady MHD stagnation point flow of Casson fluid on the shrinking/stretching surface has been investigated with the effect of thermal radiation and viscous dissipation. The governing partial differential equations are first transformed into the ordinary (similarity) differential equations. The obtained system of equations is converted from boundary value problems (BVPs) to initial value problems (IVPs) with the help of the shooting method which then solved by the RK method with help of maple software. Furthermore, the three-stage Labatto III-A method is applied to perform stability analysis with the help of a bvp4c solver in MATLAB. Current outcomes contradict numerically with published results and found inastounding agreements. The results reveal that there exist dual solutions in both shrinking and stretching surfaces. Furthermore, the temperature increases when thermal radiation, Eckert number, and magnetic number are increased. Signs of the smallest eigenvalue reveal that only the first solution is stable and can be realizable physically.
Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7
Authors: Greenfield Julia , Shang Xiaoran , Luo Heng , Zhou Yan , Linden Sara B. , Heselpoth Ryan D. , Leiman Petr G. , Nelson Daniel C. , Herzberg Osnat 
Published: September 2020

AbstractThe genome of Escherichia coli O157:H7 bacteriophage vB_EcoM_CBA120 encodes four distinct tailspike proteins (TSPs). The four TSPs, TSP1-4, attach to the phage baseplate forming a branched structure. We report the 1.9 Å resolution crystal structure of TSP2 (ORF211), the TSP that confers phage specificity towards E. coli O157:H7. The structure shows that the N-terminal 168 residues involved in TSPs complex assembly are disordered in the absence of partner proteins. The ensuing head domain contains only the first of two fold modules seen in other phage vB_EcoM_CBA120 TSPs. The catalytic site resides in a cleft at the interface between adjacent trimer subunits, where Asp506, Glu568, and Asp571 are located in close proximity. Replacement of Asp506 and Asp571 for alanine residues abolishes enzyme activity, thus identifying the acid/base catalytic machinery. However, activity remains intact when Asp506 and Asp571 are mutated into asparagine residues. Analysis of additional site-directed mutants in the background of the D506N:D571N mutant suggests engagement of an alternative catalytic apparatus comprising Glu568 and Tyr623. Finally, we demonstrate the catalytic role of two interacting glutamate residues of TSP1, located in a cleft between two trimer subunits, Glu456 and Glu483, underscoring the diversity of the catalytic apparatus employed by phage vB_EcoM_CBA120 TSPs.
Abrogation of atypical neurogenesis and vascular-derived EphA4 prevents repeated mild TBI-induced learning and memory impairments
Authors: Greer Kisha , Basso Erwin Kristobal Gudenschwager , Kelly Colin , Cash Alison , Kowalski Elizabeth , Cerna Steven , Ocampo Collin Tanchanco , Wang Xia , Theus Michelle H. 
Published: September 2020

AbstractBrain injury resulting from repeated mild traumatic insult is associated with cognitive dysfunction and other chronic co-morbidities. The current study tested the effects of aberrant neurogenesis in a mouse model of repeated mild traumatic brain injury (rmTBI). Using Barnes Maze analysis, we found a significant reduction in spatial learning and memory at 24 days post-rmTBI compared to repeated sham (rSham) injury. Cell fate analysis showed a greater number of BrdU-labeled cells which co-expressed Prox-1 in the DG of rmTBI-injured mice which coincided with enhanced cFos expression for neuronal activity. We then selectively ablated dividing neural progenitor cells using a 7-day continuous infusion of Ara-C prior to rSham or rmTBI. This resulted in attenuation of cFos and BrdU-labeled cell changes and prevented associated learning and memory deficits. We further showed this phenotype was ameliorated in EphA4f./f/Tie2-Cre knockout compared to EphA4f./f wild type mice, which coincided with altered mRNA transcript levels of MCP-1, Cx43 and TGFβ. These findings demonstrate that cognitive decline is associated with an increased presence of immature neurons and gene expression changes in the DG following rmTBI. Our data also suggests that vascular EphA4-mediated neurogenic remodeling adversely affects learning and memory behavior in response to repeated insult.
Connexin26 mediates CO2-dependent regulation of breathing via glial cells of the medulla oblongata
Authors: van de Wiel Joseph , Meigh Louise , Bhandare Amol , Cook Jonathan , Nijjar Sarbjit , Huckstepp Robert , Dale Nicholas 
Published: September 2020

AbstractBreathing is highly sensitive to the PCO2 of arterial blood. Although CO2 is detected via the proxy of pH, CO2 acting directly via Cx26 may also contribute to the regulation of breathing. Here we exploit our knowledge of the structural motif of CO2-binding to Cx26 to devise a dominant negative subunit (Cx26DN) that removes the CO2-sensitivity from endogenously expressed wild type Cx26. Expression of Cx26DN in glial cells of a circumscribed region of the mouse medulla - the caudal parapyramidal area – reduced the adaptive change in tidal volume and minute ventilation by approximately 30% at 6% inspired CO2. As central chemosensors mediate about 70% of the total response to hypercapnia, CO2-sensing via Cx26 in the caudal parapyramidal area contributed about 45% of the centrally-mediated ventilatory response to CO2. Our data unequivocally link the direct sensing of CO2 to the chemosensory control of breathing and demonstrates that CO2-binding to Cx26 is a key transduction step in this fundamental process.
The 2019/20 Australian wildfires generated a persistent smoke-charged vortex rising up to 35 km altitude
Authors: Khaykin Sergey , Legras Bernard , Bucci Silvia , Sellitto Pasquale , Isaksen Lars , Tencé Florent , Bekki Slimane , Bourassa Adam , Rieger Landon , Zawada Daniel , Jumelet Julien , Godin-Beekmann Sophie 
Published: September 2020

AbstractThe Australian bushfires around the turn of the year 2020 generated an unprecedented perturbation of stratospheric composition, dynamical circulation and radiative balance. Here we show from satellite observations that the resulting planetary-scale blocking of solar radiation by the smoke is larger than any previously documented wildfires and of the same order as the radiative forcing produced by moderate volcanic eruptions. A striking effect of the solar heating of an intense smoke patch was the generation of a self-maintained anticyclonic vortex measuring 1000 km in diameter and featuring its own ozone hole. The highly stable vortex persisted in the stratosphere for over 13 weeks, travelled 66,000 km and lifted a confined bubble of smoke and moisture to 35 km altitude. Its evolution was tracked by several satellite-based sensors and was successfully resolved by the European Centre for Medium-Range Weather Forecasts operational system, primarily based on satellite data. Because wildfires are expected to increase in frequency and strength in a changing climate, we suggest that extraordinary events of this type may contribute significantly to the global stratospheric composition in the coming decades.
MicroRNA-26a inhibits wound healing through decreased keratinocytes migration by regulating ITGA5 through PI3K/AKT signaling pathway
Authors: Jiang Zhongping , Wei Jie , Yang Weize , Li Wen , Liu Feng , Yan Xiaojie , Yan Xiaowei , Hu Niandan , Li Jia 
Published: September 2020

Abstract
Background: Keratinocyte migration is essential for skin wound healing and recent studies demonstrated that microRNAs (miRNAs) are involved in the differentiation, migration and apoptosis in keratinocytes. However, the function of miR-26a in wound healing remains to be largely explored.
Methods: Northern blot and quantitative reverse transcriptase PCR (qRT-PCR) were used to detect the miR-26a expression and Western blot was used to detect integrin α-5 (ITGA5), phosphatidylinositol-3-kinase (PI3K), p-PI3K, protein kinase B (AKT) and p-AKT protein expression in immortalized human keratinocyte cell line HaCaT and normal human epidermal keratinocytes (NHEK) after 2 ng/ml transforming growth factor-β1 (TGF-β1) treatment for 0, 6, 12 and 24 h. Transwell assay and Wound healing assay were introduced to measure the cell migration of HaCaT cells. TargetScan online database, luciferase reporter assay and RNA immunoprecipitation (RIP) were employed to confirm the relationship between miR-26a and ITGA5.
Results: The RNA expression of miR-26a was down-regulated and ITGA5 protein expression was up-regulated by TGF-β1 treatment in HaCaT and NHEK cells in a time-dependent manner. MiR-26a overexpression inhibited the migration of HaCaT cells induced by TGF-β1 while miR-26a inhibitor enhanced the migration. ITGA5 was a downstream target mRNA and regulated by miR-26a. ITGA5 overexpression reversed the inhibitory effect of miR-26a on migration in HaCaT, while ITGA5 knockdown attenuated the stimulative effect of miR-26a inhibitor in HaCaT via PI3K/AKT signaling pathway.
Conclusion: MiR-26a overexpression inhibited TGF-β1 induced HaCaT cells migration via down-regulating ITGA5 through activating the PI3K/AKT signaling pathway.
Approximate‐derivative‐based signal‐processing method to segment power‐quality disturbances
Authors: Akmaz Düzgün 
Published: September 2020

The increasing complexity of power systems and the increase in power quality (PQ) data have made it necessary to develop different and simple signal‐processing tools. In this study, an approximate‐derivative (AD) signal‐processing tool based on a simple mathematical processing approach was developed for the segmentation of PQ disturbances. Although the developed method was highly effective for the segmentation of noise‐free signals, the method was unable to properly handle the segmentation of noisy signals. Thus, to mitigate this situation, a denoising method based on the Sqtwolog threshold was applied to the noisy signals. After denoising, the proposed AD method effectively performed the segmentation. Subsequently, AD and a single‐level discrete wavelet transform (DWT) with Daubechies 4 mother wavelets were compared through simulations, which showed that successful results can be obtained using the proposed method. Furthermore, all simulations showed that the application of AD and single‐level DWT to PQ signals under different conditions resulted in similar patterns with different amplitudes. Therefore, this study provides a different approach for analysing signal using single‐level DWT.
High-energy gamma-ray study of the dynamically young SNR G150.3+4.5
Authors: Devin J. , Lemoine-Goumard M. , Grondin M.-H. , Castro D. , Ballet J. , Cohen J. , Hewitt J. W. 
Published: September 2020

Aims. The supernova remnant (SNR) G150.3+4.5 was recently discovered in the radio band; it exhibits a shell-like morphology with an angular size of ~ 3°, suggesting either an old or a nearby SNR. Extended γ-ray emission spatially coincident with the SNR was reported in the Fermi Galactic Extended Source Catalog, with a power-law spectral index of Γ = 1.91 ± 0.09. Studying particle acceleration in SNRs through their γ-ray emission is of primary concern to assess the nature of accelerated particles and the maximum energy they can reach.
Methods. Using more than ten years of Fermi-LAT data, we investigate the morphological and spectral properties of the SNR G150.3+4.5 from 300 MeV to 3 TeV. We use the latest releases of the Fermi-LAT catalog, the instrument response functions and the Galactic and isotropic diffuse emissions. We use ROSAT all-sky survey data to assess any thermal and nonthermal X-ray emission, and we derive minimum and maximum distance to G150.3+4.5.
Results. We describe the γ-ray emission of G150.3+4.5 by an extended component which is found to be spatially coincident with the radio SNR. The spectrum is hard and the detection of photons up to hundreds of GeV points towards an emission from a dynamically young SNR. The lack of X-ray emission gives a tight constraint on the ambient density n0 ≤ 3.6 × 10−3 cm−3. Since G150.3+4.5 is not reported as a historical SNR, we impose a lower limit on its age of t = 1 kyr. We estimate its distance to be between 0.7 and 4.5 kpc. We find that G150.3+4.5 is spectrally similar to other dynamically young and shell-type SNRs, such as RX J1713.7−3946 or Vela Junior. The broadband nonthermal emission is explained with a leptonic scenario, implying a downstream magnetic field of B = 5 μG and acceleration of particles up to few TeV energies.