bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new type of DNA phosphorothioation-based antiviral system in archaea
Authors: Xiong Lei , Liu Siyi , Chen Si , Xiao Yao , Zhu Bochen , Gao Yali , Zhang Yujing , Chen Beibei , Luo Jie , Deng Zixin , Chen Xiangdong , Wang Lianrong , Chen Shi 
Published: April 2019

AbstractArchaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Here we report a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication. In contrast to the breakage of invasive DNA by DndFGH in bacteria, DndCDEA-PbeABCD does not degrade or cleave viral DNA. The PbeABCD-mediated PT defence system is widespread and exhibits extensive interdomain and intradomain gene transfer events. Our results suggest that DndCDEA-PbeABCD is a new type of PT-based virus resistance system, expanding the known arsenal of defence systems as well as our understanding of host-virus interactions.
Excitation and coherent control of spin qudit modes in silicon carbide at room temperature
Authors: Soltamov V. A. , Kasper C. , Poshakinskiy A. V. , Anisimov A. N. , Mokhov E. N. , Sperlich A. , Tarasenko S. A. , Baranov P. G. , Astakhov G. V. , Dyakonov V. 
Published: April 2019

AbstractOne of the challenges in the field of quantum sensing and information processing is to selectively address and coherently manipulate highly homogeneous qubits subject to external perturbations. Here, we present room-temperature coherent control of high-dimensional quantum bits, the so-called qudits, associated with vacancy-related spins in silicon carbide enriched with nuclear spin-free isotopes. In addition to the excitation of a spectrally narrow qudit mode at the pump frequency, several other modes are excited in the electron spin resonance spectra whose relative positions depend on the external magnetic field. We develop a theory of multipole spin dynamics and demonstrate selective quantum control of homogeneous spin packets with sub-MHz spectral resolution. Furthermore, we perform two-frequency Ramsey interferometry to demonstrate absolute dc magnetometry, which is immune to thermal noise and strain inhomogeneity.
Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation
Authors: Tsytlonok Maksym , Sanabria Hugo , Wang Yuefeng , Felekyan Suren , Hemmen Katherina , Phillips Aaron H. , Yun Mi-Kyung , Waddell M. Brett , Park Cheon-Gil , Vaithiyalingam Sivaraja , Iconaru Luigi , White Stephen W. , Tompa Peter , Seidel Claus A. M. , Kriwacki Richard 
Published: April 2019

Abstractp27Kip1 is an intrinsically disordered protein (IDP) that inhibits cyclin-dependent kinase (Cdk)/cyclin complexes (e.g., Cdk2/cyclin A), causing cell cycle arrest. Cell division progresses when stably Cdk2/cyclin A-bound p27 is phosphorylated on one or two structurally occluded tyrosine residues and a distal threonine residue (T187), triggering degradation of p27. Here, using an integrated biophysical approach, we show that Cdk2/cyclin A-bound p27 samples lowly-populated conformations that provide access to the non-receptor tyrosine kinases, BCR-ABL and Src, which phosphorylate Y88 or Y88 and Y74, respectively, thereby promoting intra-assembly phosphorylation (of p27) on distal T187. Even when tightly bound to Cdk2/cyclin A, intrinsic flexibility enables p27 to integrate and process signaling inputs, and generate outputs including altered Cdk2 activity, p27 stability, and, ultimately, cell cycle progression. Intrinsic dynamics within multi-component assemblies may be a general mechanism of signaling by regulatory IDPs, which can be subverted in human disease.
Conformational dynamics of the human serotonin transporter during substrate and drug binding
Authors: Möller Ingvar R. , Slivacka Marika , Nielsen Anne Kathrine , Rasmussen Søren G. F. , Gether Ulrik , Loland Claus J. , Rand Kasper D. 
Published: April 2019

AbstractThe serotonin transporter (SERT), a member of the neurotransmitter:sodium symporter family, is responsible for termination of serotonergic signaling by re-uptake of serotonin (5-HT) into the presynaptic neuron. Its key role in synaptic transmission makes it a major drug target, e.g. for the treatment of depression, anxiety and post-traumatic stress. Here, we apply hydrogen-deuterium exchange mass spectrometry to probe the conformational dynamics of human SERT in the absence and presence of known substrates and targeted drugs. Our results reveal significant changes in dynamics in regions TM1, EL3, EL4, and TM12 upon binding co-transported ions (Na+/K+) and ligand-mediated changes in TM1, EL3 and EL4 upon binding 5-HT, the drugs S-citalopram, cocaine and ibogaine. Our results provide a comprehensive direct view of the conformational response of SERT upon binding both biologically relevant substrate/ions and ligands of pharmaceutical interest, thus advancing our understanding of the structure-function relationship in SERT.
Early warning signals of recovery in complex systems
Authors: Clements Christopher F. , McCarthy Michael A. , Blanchard Julia L. 
Published: April 2019

AbstractEarly warning signals (EWSs) offer the hope that patterns observed in data can predict the future states of ecological systems. While a large body of research identifies such signals prior to the collapse of populations, the prediction that such signals should also be present before a system’s recovery has thus far been overlooked. We assess whether EWSs are present prior to the recovery of overexploited marine systems using a trait-based ecological model and analysis of real-world fisheries data. We show that both abundance and trait-based signals are independently detectable prior to the recovery of stocks, but that combining these two signals provides the best predictions of recovery. This work suggests that the efficacy of conservation interventions aimed at restoring systems which have collapsed may be predicted prior to the recovery of the system, with direct relevance for conservation planning and policy.
Urbanity and the dynamics of language shift in Galicia
Authors: Mussa Juane Mariamo , Seoane Luis F. , Muñuzuri Alberto P. , Mira Jorge 
Published: April 2019

AbstractSociolinguistic phenomena often involve interactions across different scales and result in social and linguistic changes that can be tracked over time. Here, we focus on the dynamics of language shift in Galicia, a bilingual community in northwest Spain. Using historical data on Galician and Spanish speakers, we show that the rate at which shift dynamics unfold correlates inversely with the internal complexity of a region (approximated by the proportion of urban area). Less complex areas converge faster to steady states, while more complex ones sustain transitory dynamics longer. We further explore the contextual relevance of each region within the network of regions that constitute Galicia. The network is observed to sustain or reverse the dynamic rates. This model can introduce a competition between the internal complexity of a region and its contextual relevance in the network. Harnessing these sociodynamic features may prove useful in policy making to limit conflicts.
Flux flow spin Hall effect in type-II superconductors with spin-splitting field
Authors: Vargunin Artjom , Silaev Mikhail 
Published: April 2019

AbstractWe predict the very large spin Hall effect in type-II superconductors whose mechanism is drastically different from the previously known ones. We find that in the flux-flow regime the spin is transported by the spin-polarized Abrikosov vortices moving under the action of the Lorenz force in the direction perpendicular to the applied electric current. Due to the large vortex velocities the spin Hall angle can be of the order of unity in realistic systems based on the high-field superconductors, superconductor/ferromagnet hybrid structures or the recently developed superconductor/ferromagnetic insulator proximity structures. We propose the realization of high-frequency pure spin current generator based on the periodic structure of moving vortex lattices. We find the patterns of charge imbalance and spin accumulation generated by moving vortices, which can be used for the electrical detection of individual vortex motion. The new mechanism of inverse flux-flow spin Hall effect is found based on the driving force acting on the vortices in the presence of injected spin current which results in the generation of transverse voltage.
Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation
Authors: Jeong Hyeonsoo , Arif Bushra , Caetano-Anollés Gustavo , Kim Kyung Mo , Nasir Arshan 
Published: April 2019

AbstractHorizontal gene transfer (HGT) is widespread in the evolution of prokaryotes, especially those associated with the human body. Here, we implemented large-scale gene-species phylogenetic tree reconstructions and reconciliations to identify putative HGT-derived genes in the reference genomes of microbiota isolated from six major human body sites by the NIH Human Microbiome Project. Comparisons with a control group representing microbial genomes from diverse natural environments indicated that HGT activity increased significantly in the genomes of human microbiota, which is confirmatory of previous findings. Roughly, more than half of total genes in the genomes of human-associated microbiota were transferred (donated or received) by HGT. Up to 60% of the detected HGTs occurred either prior to the colonization of the human body or involved bacteria residing in different body sites. The latter could suggest ‘genetic crosstalk’ and movement of bacterial genes within the human body via hitherto poorly understood mechanisms. We also observed that HGT activity increased significantly among closely-related microorganisms and especially when they were united by physical proximity, suggesting that the ‘phylogenetic effect’ can significantly boost HGT activity. Finally, we identified several core and widespread genes least influenced by HGT that could become useful markers for building robust ‘trees of life’ and address several outstanding technical challenges to improve the phylogeny-based genome-wide HGT detection method for future applications.
Effects of abdominal visceral fat compared with those of subcutaneous fat on the association between PM10 and hypertension in Korean men: A cross-sectional study
Authors: Kim Hyun-Jin , Kwon Hyuktae , Jeong Su-Min , Hwang Seo Eun , Park Jin-Ho 
Published: April 2019

AbstractWe assessed whether visceral adipose tissue (VAT) compared with subcutaneous adipose tissue (SAT) has modifying effects on the cross-sectional association between ambient air pollution and hypertension in Korean men. This study included 1,417 adult men who visited a health checkup center. Abdominal fat depots were measured by computed tomography, and we used the annual average concentrations of ambient air pollutants such as particulate matter with an aerodynamic diameter of ≤10 μm (PM10), nitrogen dioxide, sulfur dioxide, and carbon monoxide (CO). The annual mean concentrations of PM10 (odds ratio [OR] = 1.30; 95% confidence interval [CI] = 1.12–1.52) and CO (OR = 1.20; 95% CI = 1.03–1.39) showed a positive association with hypertension. In particular, modifying effects on hypertension were found between PM10 and VAT-related traits such as VAT and visceral-to-subcutaneous fat ratio (VSR). The association between PM10 and hypertension was much stronger in the high-VAT (OR = 1.74; 95% CI = 1.12–2.71) and high-VSR groups (OR = 1.53; 95% CI = 1.23–1.91). However, the strength of association across levels of SAT was not observed (Pint = 0.4615). In conclusion, we found that association between PM10 exposure and hypertension is different by abdominal fat distribution.
Clinicopathological features and prognosis of young gastric cancer patients following radical gastrectomy: a propensity score matching analysis
Authors: Liu Wu , Quan Hu , Chen Xiaoyan , Ouyang Yongzhong , Xiao Hua 
Published: April 2019

AbstractThe aim of the this retrospective study was to investigate the clinicopathological features of gastric cancer (GC) in young patients and the potential impact of age on the prognosis of patients undergoing radical gastrectomy for GC. From November 2010 to November 2016, 317 young (≤45 years) and 1344 older patients (>45 years) who underwent radical gastrectomy for stage I-III GC were enrolled. The association between age and prognosis was estimated by univariate and multivariate analyses after propensity score matching (PSM). Compared with older patients, the proportion of females, poorly differentiated tumors, good nutritional status, and who received neo-adjuvant and/or adjuvant chemotherapy was significant higher in younger patients, but were less likely to suffer from comorbidities or post-operative complications (all P < 0.05). PSM analysis created 310 pairs of patients. After matching, the long-term survival in younger patients was significantly longer than in older patients at stage I, but similar at stages II and III. However, a young age was not identified as a significant prognostic factor. In conclusion, the prognosis of young GC patients is comparable with and even better than that in older patients after radical gastrectomy when matched for baseline characteristics. Early detection could improve the prognosis of young GC patients.
Highly parallel simulation and optimization of photonic circuits in time and frequency domain based on the deep-learning framework PyTorch
Authors: Laporte Floris , Dambre Joni , Bienstman Peter 
Published: April 2019

AbstractWe propose a new method for performing photonic circuit simulations based on the scatter matrix formalism. We leverage the popular deep-learning framework PyTorch to reimagine photonic circuits as sparsely connected complex-valued neural networks. This allows for highly parallel simulation of large photonic circuits on graphical processing units in time and frequency domain while all parameters of each individual component can easily be optimized with well-established machine learning algorithms such as backpropagation.
A sensitive scoring system for the longitudinal clinical evaluation and prediction of lethal disease outcomes in newborn mice
Authors: Fehlhaber Beate , Heinemann Anna S. , Rübensam Kathrin , Willers Maike , Völlger Lena , Pfeifer Sandra , von Köckritz-Blickwede Maren , Viemann Dorothee 
Published: April 2019

AbstractNeonatal animal models are increasingly employed in order to unravel age-specific disease mechanisms. Appropriate tools objectifying the clinical condition of murine neonates are lacking. In this study, we tested a scoring system specifically designed for newborn mice that relies on clinical observation and examination. Both, in a neonatal sepsis model and an endotoxic shock model, the scoring results strongly correlated with disease-induced death rates. Full as well as observation-restricted scoring, reliably predicted fatality and the remaining time until death. Clinical scores even proved as more sensitive biomarker than 6 traditionally used plasma cytokine levels in detecting sepsis at an early disease stage. In conclusion, we propose a simple scoring system that detects health impairments of newborn mice in a non-invasive longitudinal and highly sensitive manner. Its usage will help to meet animal welfare requirements and might improve the understanding of neonatal disease mechanisms.
A plasma membrane localized protein phosphatase in Toxoplasma gondii, PPM5C, regulates attachment to host cells
Authors: Yang Chunlin , Broncel Malgorzata , Dominicus Caia , Sampson Emily , Blakely William J. , Treeck Moritz , Arrizabalaga Gustavo 
Published: April 2019

AbstractThe propagation of Toxoplasma gondii is accomplished by repeated lytic cycles of parasite attachment to a host cell, invasion, replication within a parasitophorous vacuole, and egress from the cell. This lytic cycle is delicately regulated by calcium-dependent reversible phosphorylation of the molecular machinery that drives invasion and egress. While much progress has been made elucidating the protein kinases and substrates central to parasite propagation, little is known about the relevant protein phosphatases. In this study, we focused on the five protein phosphatases that are predicted to be membrane-associated either integrally or peripherally. We have determined that of these only PPM5C, a PP2C family member, localizes to the plasma membrane of Toxoplasma. Disruption of PPM5C results in a slow propagation phenotype in tissue culture. Interestingly, parasites lacking PPM5C divide and undergo egress at a normal rate, but have a deficiency in attaching to host cells. Both membrane localization and phosphatase activity are required for PPM5C’s role in attachment. Phosphoproteomic analysis show relatively few phosphorylation sites being affected by PPM5C deletion in extracellular parasites of which several are found on proteins involved in signaling cascades. This implies that PPM5C is part of a wider regulatory network important for attachment to host cells.
Fabrication of Stacked MoS2 Bilayer with Weak Interlayer Coupling by Reduced Graphene Oxide Spacer
Authors: Oh Hye Min , Kim Hyojung , Kim Hyun , Jeong Mun Seok 
Published: April 2019

AbstractWe fabricated the stacked bilayer molybdenum disulfide (MoS2) by using reduced graphene oxide (rGO) as a spacer for increasing the optoelectronic properties of MoS2. The rGO can decrease the interlayer coupling between the stacked bilayer MoS2and retain the direct band gap property of MoS2. We observed a twofold enhancement of the photoluminescence intensity of the stacked MoS2bilayer. In the Raman scattering, we observed that the E12gand A1gmodes of the stacked bilayer MoS2with rGO were further shifted compared to monolayer MoS2, which is due to the van der Waals (vdW) interaction and the strain effect between the MoS2and rGO layers. The findings of this study will expand the applicability of monolayer MoS2for high-performance optoelectronic devices by enhancing the optical properties using a vdW spacer.
Large Enriched Fragment Targeted Sequencing (LEFT-SEQ) Applied to Capture of Wolbachia Genomes
Authors: Lefoulon Emilie , Vaisman Natalie , Frydman Horacio M. , Sun Luo , Voland Lise , Foster Jeremy M. , Slatko Barton E. 
Published: April 2019

AbstractSymbiosis is a major force of evolutionary change, influencing virtually all aspects of biology, from population ecology and evolution to genomics and molecular/biochemical mechanisms of development and reproduction. A remarkable example is Wolbachia endobacteria, present in some parasitic nematodes and many arthropod species. Acquisition of genomic data from diverse Wolbachia clades will aid in the elucidation of the different symbiotic mechanisms(s). However, challenges of de novo assembly of Wolbachia genomes include the presence in the sample of host DNA: nematode/vertebrate or insect. We designed biotinylated probes to capture large fragments of Wolbachia DNA for sequencing using PacBio technology (LEFT-SEQ: Large Enriched Fragment Targeted Sequencing). LEFT-SEQ was used to capture and sequence four Wolbachia genomes: the filarial nematode Brugia malayi, wBm, (21-fold enrichment), Drosophila mauritiana flies (2 isolates), wMau (11-fold enrichment), and Aedes albopictus mosquitoes, wAlbB (200-fold enrichment). LEFT-SEQ resulted in complete genomes for wBm and for wMau. For wBm, 18 single-nucleotide polymorphisms (SNPs), relative to the wBm reference, were identified and confirmed by PCR. A limit of LEFT-SEQ is illustrated by the wAlbB genome, characterized by a very high level of insertion sequences elements (ISs) and DNA repeats, for which only a 20-contig draft assembly was achieved.
Detection of KRAS mutation via ligation-initiated LAMP reaction
Authors: Fu Yixin , Duan Xiaolei , Huang Jian , Huang Lizhen , Zhang Lutan , Cheng Wei , Ding Shijia , Min Xun 
Published: April 2019

AbstractKRAS mutations are abnormalities widely found in genomic DNA and circulating tumor DNA (ctDNA) of various types of cancers. Thus, highly sensitive detection of KRAS mutations in genomic DNA is of great significance in disease diagnosis and personalized medicine. Here, we developed a ligation-initiated loop-mediated isothermal amplification (LAMP) assaying method for ultrasensitive detection of KRAS mutation. In the presence of mutant KRAS DNA (mutDNA), the dumbbell-shaped structure (DSS) is formed by the specific ligation of two substrates (SLS1 and SLS2), which act as a template to initiate the following LAMP amplification. Making use of the outstanding specificity of ligation reaction and superior amplification of LAMP, 10 aM mutDNA can be accurately determined. In addition, as low as 0.1% mutDNA can be detected in the presence of a large excess of wild-type KRAS DNA (wtDNA), indicating the high sensitivity and specificity of the method. Furthermore, this strategy has been successfully applied for detection of a KRAS mutation from tissue samples of colorectal cancer patients. Thus, the developed ligation-initiated LAMP fluorescence assaying strategy presents a promising prospect for ultrasensitive detection of mutations.
Detection of Early-Stage Degeneration in Human Articular Cartilage by Multiparametric MR Imaging Mapping of Tissue Functionality
Authors: Nebelung Sven , Post Manuel , Knobe Matthias , Tingart Markus , Emans Pieter , Thüring Johannes , Kuhl Christiane , Truhn Daniel 
Published: April 2019

AbstractTo assess human articular cartilage tissue functionality by serial multiparametric quantitative MRI (qMRI) mapping as a function of histological degeneration. Forty-nine cartilage samples obtained during total knee replacement surgeries were placed in a standardized artificial knee joint within an MRI-compatible compressive loading device and imaged in situ and at three loading positions, i.e. unloaded, at 2.5 mm displacement (20% body weight [BW]) and at 5 mm displacement (110% BW). Using a clinical 3.0 T MRI system (Achieva, Philips), serial T1, T1ρ, T2 and T2* maps were generated for each sample and loading position. Histology (Mankin scoring) and biomechanics (Young’s modulus) served as references. Samples were dichotomized as intact (int, n = 27) or early degenerative (deg, n = 22) based on histology and analyzed using repeated-measures ANOVA and unpaired Student’s t-tests after log-transformation. For T1ρ, T2 and T2*, significant loading-induced differences were found in deg (in contrast to int) samples, while for T1 significant decreases in all zones were observed, irrespective of degeneration. In conclusion, cartilage functionality may be visualized using serial qMRI parameter mapping and the response-to-loading patterns are associated with histological degeneration. Hence, loading-induced changes in qMRI parameter maps provide promising surrogate parameters of tissue functionality and status in health and disease.