bluuebunny/crossref_metadata_2025_split huggingface dataset:
Propagation of Activated B Cells by In Vitro Severe Fever With Thrombocytopenia Syndrome Virus Infection of Human Peripheral Blood Mononuclear Cells
Authors: Wada Yuji , Miyamoto Sho , Iida Shun , Sano Kaori , Sato Yuko , Ainai Akira , Saito Kumpei , Katano Harutaka , Hasegawa Hideki , Suzuki Tadaki 
Published: July 2021

AbstractSevere fever with thrombocytopenia syndrome (SFTS) is an emerging, life-threatening tick-borne viral hemorrhagic fever caused by SFTS virus (SFTSV). Transient appearance of plasmablastic lymphocytes in the peripheral blood of SFTS cases has been reported; however, the pathological significance of this transient burst in peripheral blood plasmablastic lymphocytes is unclear. Here, we show that SFTSV infection of human peripheral blood mononuclear cells in vitro induced propagation of atypical lymphocytes. These atypical lymphocytes were activated B cells, which were induced by secretory factors other than viral particles; these factors were secreted by SFTSV-infected B cells. Activated B cells shared morphological and immunophenotypic characteristics with B cells of plasmablast lineage observed in peripheral blood and autopsy tissues of SFTS cases. This suggests that SFTSV-infected B cells secrete factors that induce B-cell differentiation to plasmablasts, which may play an important role in pathogenesis of SFTS through the SFTSV-B cell axis.
Flooding mechanism of biolithite based on progressive ion exchange model: an example of the Wangxuzhuang biolithite reservoir in the Dagang oilfield
Authors: Sun Jianmeng , Lv Xindi , Zong Jie , Ma Shuiping , Wu Yong , Huang Xiaodi , Chi Ming , Feng Xueyin , Yan Weichao 
Published: July 2021

Abstract
The biolithite reservoir has a strong heterogeneity and complex pore structure, and the changing trend of formation resistivity is complicated during the waterflood development process. In the logging interpretation of a water-flooded layer, mixed-formation water resistivity is a critical parameter and its accurate calculation heavily influences the evaluation of logging water saturation. The commonly used mixed liquid resistivity models have not taken into account the contribution of irreducible clay water and, thus, they are not suitable for biolithite reservoirs with high shale contents. In this paper, a new 3D digital core was constructed based on CT scanning, and a progressive ion exchange model of the mixed-formation water compatible with the biolithite reservoir put forward. Compared with experimental data from core water flooding, the progressive ion exchange model conforms to the resistivity change law of biolithite reservoirs. Through numerical simulation and analysis of the resistivity of biolithite reservoir, it is concluded that the salinity of injected water and the formation water saturation are the main factors affecting the resistivity characteristics of water-flooded layer. In terms of the interpretation of the water-flooded layer, the water saturation was calculated using the progressive ion exchange model through finite element modelling of formation resistivity. The particular mechanism of water flooding and changing law of rock electrical properties during reservoir water injection development are presented, which provide a new reliable basis for optimization of the biolithite reservoir development plan.
Vibration and horizontal directivity analysis of transmitting transducer for acoustic logging while drilling
Authors: Gou Yang , Fu Xin 
Published: July 2021

Abstract
Radially polarized open-cylindrical piezoelectric transducers are widely used in the field of acoustic logging while drilling (LWD). Unlike the wireline logging transducer, the structure of the acoustic LWD transducer is an open structure; in this case, its radial vibration is accompanied by apparent circumferential vibration. In this paper, based on the two-dimensional wave equations and electrostatic charge equation, according to the free boundary conditions of the transducer, the resonance frequency equation of radial-circumferential coupled vibration for the acoustic LWD transducer is obtained. The vibration modal and resonance frequency for transducers of several typical sizes are simulated using COMSOL software. The results show that when the geometrical size of the transducer satisfies certain conditions, the theoretical calculation and the numerical analysis are in good agreement and the relative error is controlled below 3%. Meanwhile, the horizontal directivity of the LWD transducer after actual installation is discussed, and it is found that adding appropriate coupling materials can improve the monopole sound field radiation. So, it is expected that this work can serve as a reference for the acoustic LWD transducer design and install.
Effect of orbital trapping by bar resonances in the local U–V velocity field
Authors: Moreno Edmundo , Fernández-Trincado José G , Schuster William J , Pérez-Villegas Angeles , Chaves-Velasquez Leonardo 
Published: July 2021

ABSTRACT
The effects in the local U–V velocity field due to orbital trapping by bar resonances have been studied computing 15 resonant families in a non-axisymmetric Galactic potential, considering the bar’s angular velocity between 35 and 57.5 ${\rm \, km\, s^{-1}{kpc}^{-1}}$. Only cases in the low, 37.5, 40 ${\rm \, km\, s^{-1}{kpc}^{-1}}$, and high, 55, 57.5 ${\rm \, km\, s^{-1}{kpc}^{-1}}$, velocity ranges give trapping structures that have some similarity with observed features in the velocity distribution. The resulting structures in the local U–V plane form resonant bands appearing at various levels in velocity V. Cases with angular velocity 40 and 55 ${\rm \, km\, s^{-1}{kpc}^{-1}}$ show the greatest similarity with observed branches. Our best approximation to the local velocity field by orbital trapping is obtained with a bar angular velocity of 40 ${\rm \, km\, s^{-1}{kpc}^{-1}}$ and a bar angle of 40°. With this solution, three main observed features can be approximated: (i) the Hercules branch at V = $-50\, {\rm \, km\, s^{-1}}$ produced by the resonance 8/1 outside corotation, and the close features produced by resonances 5/1 and 6/1, (ii) the newly detected low-density arch at V ≃ 40 ${\rm \, km\, s^{-1}}$ produced approximately by the resonance 4/3, (iii) the inclined structure below the Hercules branch, also observed in the Gaia DR2 data, produced by tube orbits around Lagrange point L5 at corotation. Some predicted contributions due to orbital trapping in regions of the U–V plane corresponding to the Galactic halo are given, which could help to further restrict the value of the angular velocity of the Galactic bar. No support by orbital trapping is found for the Arcturus stream at V$\approx \, -100\, {\rm \, km\, s^{-1}}$.
GmPIN-dependent polar auxin transport is involved in soybean nodule development
Authors: Gao Zhen , Chen Zhiwei , Cui Yuanyuan , Ke Meiyu , Xu Huifang , Xu Qinzhen , Chen Jiaomei , Li Yang , Huang Laimei , Zhao Hong , Huang Dingquan , Mai Siyuan , Xu Tao , Liu Xiao , Li Shujia , Guan Yuefeng , Yang Wenqiang , Friml Jiří , Petrášek Jan , Zhang Jing , Chen Xu 
Published: July 2021

Abstract
To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that are fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed the impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that the establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia.
The mediating role of epigenetic clocks underlying educational inequalities in mortality: a multi-cohort study
Authors: Fiorito Giovanni , Pedron Sara , Ochoa-Rosales Carolina , McCrory Cathal , Polidoro Silvia , Zhang Yan , Dugué Pierre-Antoine , Ratliff Scott , Zhao Wei , McKay Gareth J , Costa Giuseppe , Solinas Maria Giuliana , Harris Kathleen Mullan , Tumino Rosario , Grioni Sara , Ricceri Fulvio , Panico Salvatore , Brenner Hermann , Schwettmann Lars , Waldenberger Melanie , Matias-Garcia Pamela R , Peters Annette , Hodge Allison , Giles Graham G , Schmitz Lauren L. , Levine Morgan , Smith Jennifer , Liu Yongmei , Kee Frank , Young Ian , McGuinness Bernadette , McKnight Amy Jayne , van Meurs Joyce , Voortman Trudy , Kenny Rose A ,   Lifepath consortium, Vineis Paolo , Carmeli Cristian 
Published: July 2021

AbstractEducational inequalities in mortality have been observed for decades, however the underlying biological mechanisms are not well known. We assessed the mediating role of altered aging of immune cells functioning captured by DNA methylation changes in blood (known as epigenetic clocks) in educational associated all-cause mortality. Data were from eight prospective population-based cohort studies, representing 13,021 participants. We found educational inequalities in mortality were larger for men than for women, estimated by hazard differences and ratios. Epigenetic clocks explained approximately 50% of educational inequalities in mortality for men, while the proportion was small for women. Most of this mediation was explained by differential effects of unhealthy lifestyles and morbidities of the WHO risk factors for premature mortality. These results support DNA methylation-based epigenetic aging as a signature of educational inequalities in life expectancy emphasizing the need for policies to address the unequal social distribution of these WHO risk factors.
Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages
Authors: Petrone Mary E. , Rothman Jessica E. , Breban Mallery I. , Ott Isabel M. , Russell Alexis , Lasek-Nesselquist Erica , Kelly Kevin , Omerza Greg , Renzette Nicholas , Watkins Anne E. , Kalinich Chaney C. , Alpert Tara , Brito Anderson F. , Earnest Rebecca , Tikhonova Irina R. , Castaldi Christopher , Kelly John P. , Shudt Matthew , Plitnick Jonathan , Schneider Erasmus , Murphy Steven , Neal Caleb , Laszlo Eva , Altajar Ahmad , Pearson Claire , Muyombwe Anthony , Downing Randy , Razeq Jafar , Niccolai Linda , Wilson Madeline S. , Anderson Margaret L. , Wang Jianhui , Liu Chen , Hui Pei , Mane Shrikant , Taylor Bradford P. , Hanage William P. , Landry Marie L. , Peaper David R. , Bilguvar Kaya , Fauver Joseph R. , Vogels Chantal B.F. , Gardner Lauren M. , Pitzer Virginia E. , George Kirsten St. , Adams Mark D. , Grubaugh Nathan D. 
Published: July 2021

AbstractEmerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting response efforts when community transmission is detected. However, this assessment requires that a true comparison can be made between the new variant and its predecessors because factors other than the virus genotype may influence spread and transmission. In this study, we develop a framework that integrates genomic surveillance data to estimate the relative effective reproduction number (Rt) of co-circulating lineages. We use Connecticut, a state in the northeastern United States in which the SARS-CoV-2 variants B.1.1.7 and B.1.526 co-circulated in early 2021, as a case study for implementing this framework. We find that the Rt of B.1.1.7 was 6-10% larger than that of B.1.526 in Connecticut in the midst of a COVID-19 vaccination campaign. To assess the generalizability of this framework, we apply it to genomic surveillance data from New York City and observe the same trend. Finally, we use discrete phylogeography to demonstrate that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of B.1.1.7 were larger than those resulting from B.1.526 introductions. Our framework, which uses open-source methods requiring minimal computational resources, may be used to monitor near real-time variant dynamics in a myriad of settings.
Machine learning of all Mycobacterium tuberculosis H37Rv RNA-seq data reveals a structured interplay between metabolism, stress response, and infection
Authors: Yoo Reo , Rychel Kevin , Poudel Saugat , Al-bulushi Tahani , Yuan Yuan , Chauhan Siddharth , Lamoureux Cameron , Palsson Bernhard O. , Sastry Anand 
Published: July 2021

AbstractMycobacterium tuberculosis is one of the most consequential human bacterial pathogens, posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its ability to adapt its transcriptional response to environmental stresses through its transcriptional regulatory network (TRN). While many studies have sought to characterize specific portions of the M. tuberculosis TRN, a systems level characterization and analysis of interactions among the controlling transcription factors remains to be achieved. Here, we applied an unsupervised machine learning method to modularize the M. tuberculosis transcriptome and describe the role of transcription factors (TFs) in the TRN. By applying Independent Component Analysis (ICA) to over 650 transcriptomic samples, we obtained 80 independently modulated gene sets known as “iModulons,” many of which correspond to known regulons. These iModulons explain 61% of the variance in the organism’s transcriptional response. We show that iModulons: 1) reveal the function of previously unknown regulons, 2) describe the transcriptional shifts that occur during environmental changes such as shifting carbon sources, oxidative stress, and virulence events, and 3) identify intrinsic clusters of transcriptional regulons that link several important metabolic systems, including lipid, cholesterol, and sulfur metabolism. This transcriptome-wide analysis of the M. tuberculosis TRN informs future research on effective ways to study and manipulate its transcriptional regulation, and presents a knowledge-enhanced database of all published high-quality RNA-seq data for this organism to date.
Behaviourally modulated hippocampal theta oscillations in the ferret persist during both locomotion and immobility
Authors: Dunn S.L.S. , Town S.M. , Bizley J.K. , Bendor D. 
Published: July 2021

AbstractTheta oscillations are a hallmark of hippocampal activity across mammals and play a critical role in many hippocampal models of memory and spatial navigation. To reconcile the cross-species differences observed in the presence and properties of theta, we recorded hippocampal local field potentials in rats and ferrets during auditory and visual localisation tasks designed to vary locomotion and sensory attention. Here, we show that theta oscillations occur during locomotion in both ferrets and rats, however during periods of immobility, theta oscillations persisted in the ferret, contrasting starkly with the switch to large irregular activity (LIA) in the rat. Theta during immobility in the ferret was identified as analogous to Type 2 theta that has been observed in rodents due to its sensitivity to atropine, and was modulated by behavioural state, with the strongest theta observed during reward epochs. These results demonstrate that even under similar behavioural conditions, differences exist between species in the relationship between theta and behavioural state.
High confidence identification of intra-host single nucleotide variants for person-to-person influenza transmission tracking in congregate settings
Authors: Berry Irina Maljkovic , Treangen Todd , Fung Christian , Tai Sheldon , Pollett Simon , Hong Filbert , Li Tao , Pireku Papa , Thomanna Ashley , German Jennifer , de Mesquita P. Jacob Bueno , Rutvisuttinunt Wiriya , Panciera Michael , Lidl Grace , Frieman Matthew , Jarman Richard G , Milton Donald K ,   Prometheus@UMD Consortium
Published: July 2021

ABSTRACTInfluenza within-host viral populations are the source of all global influenza diversity and play an important role in driving the evolution and escape of the influenza virus from human immune responses, antiviral treatment, and vaccines, and have been used in precision tracking of influenza transmission chains. Next Generation Sequencing (NGS) has greatly improved our ability to study these populations, however, major challenges remain, such as accurate identification of intra-host single nucleotide variants (iSNVs) that represent within-host viral diversity of influenza virus. In order to investigate the sources and the frequency of called iSNVs in influenza samples, we used a set of longitudinal influenza patient samples collected within a University of Maryland (UMD) cohort of college students in a living learning community. Our results indicate that technical replicates aid in removal of random RT-PCR, PCR, and platform sequencing errors, while the use of clonal plasmids for removal of systematic errors is more important in samples of low RNA abundance. We show that the choice of reference for read mapping affects the frequency of called iSNVs, with the sample self-reference resulting in the lowest amount of iSNV noise. The importance of variant caller choice is also highlighted in our study, as we observe differential sensitivity of variant callers to the mapping reference choice, as well as the poor overlap of their called iSNVs. Based on this, we develop an approach for identification of highly probable iSNVs by removal of sequencing and bioinformatics algorithm-associated errors, which we implement in phylogenetic analyses of the UMD samples for a greater resolution of transmission links. In addition to identifying closely related transmission connections supported by the presence of highly confident shared iSNVs between patients, our results also indicate that the rate of minor variant turnover within a host may be a limiting factor for utilization of iSNVs to determine patient epidemiological links.
Uncontrolled CD21low age-associated and B1 B cell accumulation caused by failure of an EGR2/3 tolerance checkpoint
Authors: Masle-Farquhar Etienne , Peters Timothy J. , Miosge Lisa A. , Parish Ian A. , Weigel Christoph , Oakes Christopher C. , Reed Joanne H. , Goodnow Christopher C. 
Published: July 2021

SUMMARYCD21low age-associated or atypical memory B cells, enriched for autoantibodies and poised for plasma cell differentiation, accumulate in large numbers in chronic infections, autoimmune disease and immunodeficiency, posing the question of what checkpoints normally oppose their excessive accumulation. Here, we reveal a critical role for the calcium-NFAT-regulated transcription factors EGR2 and EGR3. In the absence of EGR2 and EGR3 within B cells, CD21low and B1 B cells accumulate and circulate in young mice in numbers 10-20 times greater than normal, over-express a large set of EGR2 ChIP-seq target genes including known drivers of plasma cell differentiation and under-express drivers of follicular germinal centers. Most follicular B cells constitutively express Egr2 proportionally to surface IgM down-regulation by self-antigens, and EGR2/3 deficiency abolishes this characteristic anergy response. These results define a key transcriptional checkpoint repressing CD21low B cell formation and inform how NFATC1 or EGR2 mutations promote B1 cell-derived chronic lymphocytic leukemias.
Identifying components that vary in space and time from resting-state functional MRI
Authors: Scott Gregory , Leech Rob 
Published: July 2021

AbstractA widespread assumption of fMRI-derived large-scale intrinsic connectivity networks (ICNs) is that they are spatially static over time. However, the assumption of spatial stationarity of ICNs has been challenged by a range of techniques that allow for time-varying connectivity between brain regions and demonstration that canonical networks like the default model network (DMN) can be fractionated according to time-varying connectivity relationships of their subcomponents. Previously, we developed a simple spatiotemporal ICA (stICA) technique to allow the discovery of patterns of spatiotemporal evolution in task fMRI data in a way that avoided the traditional constraint of spatial stationarity on brain networks, and we validated the approach in fMRI of task-to-rest transitions. Here, we apply our stICA technique to resting-state fMRI datasets to explore whether spatiotemporally evolving components of brain activity can be identified in the absence of an overt behavioural task. We found that stICA components could generally be described in terms of graded onsets and offsets of ICNs that had been calculated based on techniques that assumed spatial stationarity. Our results suggest that, to a reasonable approximation, stable ICNs can be taken to be building blocks of the spatiotemporal patterns measured with resting-state fMRI.
Using stationary vital rates in impact assessments may underestimate potential threat
Authors: Horswill C. , Miller J.A.O. , Wood M. J. 
Published: July 2021

AbstractPopulation viability analysis (PVA) is commonly used to assess future potential risks to threatened species. These models are typically based on mean vital rates, such as survival and fecundity, with some level of environmental stochasticity. However, the vital rates of wild populations, especially those already exhibiting declining trajectories, may be nonstationary, such that the mean or variance changes over time. In this study, we examined whether including observed temporal trends in vital rates affects the predictive accuracy of PVA, as well as the projected impact associated with a hypothetical threat. To achieve this, we ran a series of simulations using Leslie matrix PVA models that included different combinations of environmental stochasticity, temporal trends in vital rates, and threat. We apply our analysis to a long-lived colonial species of seabird, the black-legged kittiwake Rissa tridactyla, that is classified as globally Vulnerable and is potentially highly sensitive to offshore renewable energy development. We found that including observed temporal trends in vital rates was (i) crucial for the accurate reconstruction of observed population dynamics and (ii) had a dramatic effect on the projected impact from the hypothetical threat. In an era when many animal and plant populations are declining due to long-term trends in their vital rates, we identify that including this demographic structure is essential for robustly evaluating potential threats using PVA models. Omitting observed temporal trends in vital rates from impact assessments is highly likely to yield unreliable results that could misinform conservation and management decision making. This result has immediate application for conducting impact assessments on protected species and populations.