bluuebunny/crossref_metadata_2025_split huggingface dataset:
Particle Trapping in Axisymmetric Electron Holes
Authors: Hutchinson I. H. 
Published: July 2020

AbstractElectron orbits are calculated in solitary two‐dimensional axisymmetric electrostatic potential structures, typical of plasma electron holes, in order to establish the conditions for the particles to remain trapped. Analytic calculations of the evolution of the parallel energy caused by the perturbing radial electric field (breaking magnetic moment invariance) are shown to agree well with full numerical orbit integration Poincaré plots. The predominant mechanism of detrapping is resonance between the gyrofrequency in the parallel magnetic field and harmonics of the parallel bounce frequency. A region of phase space adjacent to the trapped‐passing boundary in parallel energy is generally stochastic because of island overlap of different harmonics, but except for very strong radial electric field perturbation, more deeply trapped orbits have well‐defined islands and are permanently confined. A simple universal quantitative algorithm is given, and its results plotted as a function of magnetic field strength and hole radial scale length, determining the phase space volume available to sustain the electron hole by depression of the permanently trapped distribution function.
Quiet Time Ionopheric Irregularities Over the African Equatorial Ionization Anomaly Region
Authors: Amaechi Paul O. , Oyeyemi Elijah O. , Akala Andrew O. , Falayi Elijah O. , Kaab Mohamed , Benkhaldoun Zouhair , Mazaudier Christine‐Amory 
Published: July 2020

AbstractThis paper investigated variations of quiet time ionospheric irregularities over the African equatorial ionization anomaly using the rate of change of total electron content index. Irregularities were quantified in terms of percentage occurrence and examined along with parameter of the anomaly, mainly its strength and the asymmetry of the crests as well as equatorial electric field derived from the real‐time equatorial electric field model and meridional wind obtained from the horizontal wind model. Irregularities occurred from 19:30 to 03:00 LT with a time difference of 1 hr between both crests. The highest occurrences were registered in April: 91.67%, 75.00%, and 96.43% for the northern crest, trough, and southern crest, respectively. Seasonally, stronger anomaly (>20 total electron content unit) in addition to the highest equatorial electric field value in the dusk sector corresponded with the equinoctial higher occurrence rate in both hemispheres, while stronger meridional wind and farthest crests location accounted for the least occurrence in winter. The summer occurrence rate was favored by reduced meridional wind, smaller crests location, and late time of prereversal enhancement at the magnetic equator. There was a significant asymmetry in irregularities over the crests in both hemispheres with stronger and greater occurrence rate over the southern crest. Also, irregularities strength and occurrence rate were similar over the northern crest and trough in summer. In addition to dusk‐sector activity, irregularities occurred during postmidnight in summer. Simultaneous variations of irregularities at the crests and trough also highlighted the contribution of nonequatorial processes to their formation at the crests.
Deciphering the star codings: astrocyte manipulation alters mouse behavior
Authors: Park Keebum , Lee Sung Joong 
Published: July 2020

AbstractAstrocytes occupy a vast area within the central nervous system (CNS). Despite their abundance, the functional role of astrocytes in vivo has only begun to be uncovered. Astrocytes were typically thought to be involved in pathophysiological states. However, recent studies have shown that astrocytes are actively involved in cell signaling in normal physiological states; manipulating various aspects of astrocytic cell signaling in vivo has revealed that astrocytes are key players in controlling healthy behavior in the absence of pathophysiology. Unfortunately, the study of astrocyte function is often limited by the number of approaches available due to our lack of understanding of cell physiology. This review summarizes recent studies in which altered astrocyte signaling capacity resulted in dramatic changes in behavior. We not only discuss the methodologies available to manipulate astrocytes but also provide insights into the behavioral roles of astrocytes in the CNS.
Apoptotic cell therapy for cytokine storm associated with acute severe sepsis
Authors: Karbian Netanel , Abutbul Avraham , el-Amore Raja , Eliaz Ran , Beeri Ronen , Reicher Barak , Mevorach Dror 
Published: July 2020

AbstractSepsis has no proven pharmacologic treatment other than appropriate antibiotic agents, fluids, vasopressors as needed, and possibly corticosteroids. It is generally initiated mainly by the simultaneous recognition by various components of the innate immune system of either pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns (DAMPs). In the current study, we employed the murine cecal ligation and puncture (CLP) model for sepsis to evaluate the effect of post-CLP infusion of apoptotic cells (Allocetra-OTS) on a CLP severe sepsis model. Cardiovascular evaluation, acute kidney injury (AKI), acute liver injury (ALI), and hematological and metabolic function were evaluated. Cytokine and chemokine profiles were measured by Multiplex ELISA and mitochondrial function, and glycolysis by Seahorse. The Murine Sepsis Score (MSS) was used for disease severity definition. CLP mice had low blood pressure, poor cardiac output, and lung dysfunction, as well as AKI, ALI, and thrombocytopenia, which correlated with the MSS and corresponded to a cytokine/chemokine storm. Apoptotic cell administration markedly improved the cytokine and chemokine storm and restored the impaired mitochondrial and glycolytic function in white blood cells leading to increased survival, from 6 to 60% (P < 0.0001), together with a significant improvement in organ dysfunction. We conclude that the deleterious immune response in CLP-induced sepsis can be successfully modified by apoptotic cell infusion.
Tumor response and endogenous immune reactivity after administration of HER2 CAR T cells in a child with metastatic rhabdomyosarcoma
Authors: Hegde Meenakshi , Joseph Sujith K. , Pashankar Farzana , DeRenzo Christopher , Sanber Khaled , Navai Shoba , Byrd Tiara T. , Hicks John , Xu Mina L. , Gerken Claudia , Kalra Mamta , Robertson Catherine , Zhang Huimin , Shree Ankita , Mehta Birju , Dakhova Olga , Salsman Vita S. , Grilley Bambi , Gee Adrian , Dotti Gianpietro , Heslop Helen E. , Brenner Malcolm K. , Wels Winfried S. , Gottschalk Stephen , Ahmed Nabil 
Published: July 2020

AbstractRefractory metastatic rhabdomyosarcoma is largely incurable. Here we analyze the response of a child with refractory bone marrow metastatic rhabdomyosarcoma to autologous HER2 CAR T cells. Three cycles of HER2 CAR T cells given after lymphodepleting chemotherapy induces remission which is consolidated with four more CAR T-cell infusions without lymphodepletion. Longitudinal immune-monitoring reveals remodeling of the T-cell receptor repertoire with immunodominant clones and serum autoantibodies reactive to oncogenic signaling pathway proteins. The disease relapses in the bone marrow at six months off-therapy. A second remission is achieved after one cycle of lymphodepletion and HER2 CAR T cells. Response consolidation with additional CAR T-cell infusions includes pembrolizumab to improve their efficacy. The patient described here is a participant in an ongoing phase I trial (NCT00902044; active, not recruiting), and is 20 months off T-cell infusions with no detectable disease at the time of this report.
Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping
Authors: Höllerer Simon , Papaxanthos Laetitia , Gumpinger Anja Cathrin , Fischer Katrin , Beisel Christian , Borgwardt Karsten , Benenson Yaakov , Jeschek Markus 
Published: July 2020

AbstractPredicting effects of gene regulatory elements (GREs) is a longstanding challenge in biology. Machine learning may address this, but requires large datasets linking GREs to their quantitative function. However, experimental methods to generate such datasets are either application-specific or technically complex and error-prone. Here, we introduce DNA-based phenotypic recording as a widely applicable, practicable approach to generate large-scale sequence-function datasets. We use a site-specific recombinase to directly record a GRE’s effect in DNA, enabling readout of both sequence and quantitative function for extremely large GRE-sets via next-generation sequencing. We record translation kinetics of over 300,000 bacterial ribosome binding sites (RBSs) in >2.7 million sequence-function pairs in a single experiment. Further, we introduce a deep learning approach employing ensembling and uncertainty modelling that predicts RBS function with high accuracy, outperforming state-of-the-art methods. DNA-based phenotypic recording combined with deep learning represents a major advance in our ability to predict function from genetic sequence.
A STING-based biosensor affords broad cyclic dinucleotide detection within single living eukaryotic cells
Authors: Pollock Alex J. , Zaver Shivam A. , Woodward Joshua J. 
Published: July 2020

AbstractCyclic dinucleotides (CDNs) are second messengers conserved across all three domains of life. Within eukaryotes they mediate protective roles in innate immunity against malignant, viral, and bacterial disease, and exert pathological effects in autoimmune disorders. Despite their ubiquitous role in diverse biological contexts, CDN detection methods are limited. Here, using structure guided design of the murine STING CDN binding domain, we engineer a Förster resonance energy transfer (FRET) based biosensor deemed BioSTING. Recombinant BioSTING affords real-time detection of CDN synthase activity and inhibition. Expression of BioSTING in live human cells allows quantification of localized bacterial and eukaryotic CDN levels in single cells with low nanomolar sensitivity. These findings establish BioSTING as a powerful kinetic in vitro platform amenable to high throughput screens and as a broadly applicable cellular tool to interrogate the temporal and spatial dynamics of CDN signaling in a variety of infectious, malignant, and autoimmune contexts.
Cross-serotype protection against group A Streptococcal infections induced by immunization with SPy_2191
Authors: Sanduja Pooja , Gupta Manish , Somani Vikas Kumar , Yadav Vikas , Dua Meenakshi , Hanski Emanuel , Sharma Abhinay , Bhatnagar Rakesh , Johri Atul Kumar 
Published: July 2020

AbstractGroup A Streptococcus (GAS) infection causes a range of diseases, but vaccine development is hampered by the high number of serotypes. Here, using reverse vaccinology the authors identify SPy_2191 as a cross-protective vaccine candidate. From 18 initially identified surface proteins, only SPy_2191 is conserved, surface-exposed and inhibits both GAS adhesion and invasion. SPy_2191 immunization in mice generates bactericidal antibodies resulting in opsonophagocytic killing of prevalent and invasive GAS serotypes of different geographical regions, including M1 and M49 (India), M3.1 (Israel), M1 (UK) and M1 (USA). Resident splenocytes show higher interferon-γ and tumor necrosis factor-α secretion upon antigen re-stimulation, suggesting activation of cell-mediated immunity. SPy_2191 immunization significantly reduces streptococcal load in the organs and confers ~76-92% protection upon challenge with invasive GAS serotypes. Further, it significantly suppresses GAS pharyngeal colonization in mice mucosal infection model. Our findings suggest that SPy_2191 can act as a universal vaccine candidate against GAS infections.
RETRACTED ARTICLE: Ornithine-A urea cycle metabolite enhances autophagy and controls Mycobacterium tuberculosis infection
Authors: Sivangala Thandi Ramya , Radhakrishnan Rajesh Kumar , Tripathi Deepak , Paidipally Padmaja , Azad Abul K. , Schlesinger Larry S. , Samten Buka , Mulik Sachin , Vankayalapati Ramakrishna 
Published: July 2020

AbstractMacrophages are professional phagocytes known to play a vital role in controllingMycobacterium tuberculosis(Mtb) infection and disease progression. Here we compareMtbgrowth in mouse alveolar (AMs), peritoneal (PMs), and liver (Kupffer cells; KCs) macrophages and in bone marrow-derived monocytes (BDMs). KCs restrictMtbgrowth more efficiently than all other macrophages and monocytes despite equivalent infections through enhanced autophagy. A metabolomics comparison ofMtb-infected macrophages indicates that ornithine and imidazole are two top-scoring metabolites inMtb-infected KCs and that acetylcholine is the top-scoring inMtb-infected AMs. Ornithine, imidazole and atropine (acetylcholine inhibitor) inhibitMtbgrowth in AMs. Ornithine enhances AMPK mediated autophagy whereas imidazole directly killsMtbby reducing cytochrome P450 activity. Intranasal delivery of ornithine or imidazole or the two together restrictsMtbgrowth. Our study demonstrates that the metabolic differences betweenMtb-infected AMs and KCs lead to differences in the restriction ofMtbgrowth.
Structurally divergent dynamic combinatorial chemistry on racemic mixtures
Authors: Gianga Tiberiu-M. , Pantoș G. Dan 
Published: July 2020

AbstractStructurally Divergent Reactions on Racemic Mixtures are atypical processes in Nature. The few examples reported in the literature take place in organic solvents and are driven by the reagents’ interaction with bulky chiral catalysts. Herein, we describe a dynamic combinatorial approach to generate structural divergence from racemic building blocks. The divergence is due to a stereospecific electron-donor – electron-acceptor interaction of diastereomeric macrocycles, leading to structurally distinct pseudorotaxanes. The equilibrated dynamic combinatorial library contains, amongst various macrocycles, two different types of [2]catenanes that are non-isomeric. The formation of these [2]catenanes is due to a spontaneous stereo and structurally divergent assembly of the building blocks.
Lactate released by inflammatory bone marrow neutrophils induces their mobilization via endothelial GPR81 signaling
Authors: Khatib-Massalha Eman , Bhattacharya Suditi , Massalha Hassan , Biram Adi , Golan Karin , Kollet Orit , Kumari Anju , Avemaria Francesca , Petrovich-Kopitman Ekaterina , Gur-Cohen Shiri , Itkin Tomer , Brandenburger Isabell , Spiegel Asaf , Shulman Ziv , Gerhart-Hines Zachary , Itzkovitz Shalev , Gunzer Matthias , Offermanns Stefan , Alon Ronen , Ariel Amiram , Lapidot Tsvee 
Published: July 2020

AbstractNeutrophils provide first line of host defense against bacterial infections utilizing glycolysis for their effector functions. How glycolysis and its major byproduct lactate are triggered in bone marrow (BM) neutrophils and their contribution to neutrophil mobilization in acute inflammation is not clear. Here we report that bacterial lipopolysaccharides (LPS) orSalmonellaTyphimurium triggers lactate release by increasing glycolysis, NADPH-oxidase-mediated reactive oxygen species and HIF-1α levels in BM neutrophils. Increased release of BM lactate preferentially promotes neutrophil mobilization by reducing endothelial VE-Cadherin expression, increasing BM vascular permeability via endothelial lactate-receptor GPR81 signaling. GPR81−/−mice mobilize reduced levels of neutrophils in response to LPS, unless rescued by VE-Cadherin disrupting antibodies. Lactate administration also induces release of the BM neutrophil mobilizers G-CSF, CXCL1 and CXCL2, indicating that this metabolite drives neutrophil mobilization via multiple pathways. Our study reveals a metabolic crosstalk between lactate-producing neutrophils and BM endothelium, which controls neutrophil mobilization under bacterial infection.
Enhancing power factor of SnSe sheet with grain boundary by doping germanium or silicon
Authors: Sun Jie , Yu Jiabing , Guo Yaguang , Wang Qian 
Published: July 2020

AbstractGrain boundaries (GBs) widely exist in two-dimensional (2D) and three-dimensional (3D) materials in experiment, which significantly affect the thermoelectric performance because of the scattering effect on the transport of both electron and phonon. Motivated by the research progress in 3D SnSe, we have systematically studied the GBs in a SnSe monolayer including their stable geometric configurations, the effect of GBs on power factor and Seebeck coefficient, and the strategies to improve the performance by using first principles calculations combined with semiclassical Boltzmann theory. We find that the GBs increase the potential energy barrier of carriers and decrease the valley degeneracy of the conducting bands, leading to the reduction of Seebeck coefficient, as compared to that of the pristine SnSe sheet. We further demonstrate that the trapping gap states are effectively eliminated or reduced by doping germanium or silicon, leading to the enhanced electrical conductivity, power factor, and Seebeck coefficient. These findings shed lights on developing practical strategies for modulating the thermoelectric performance of 2D polycrystalline sheets.
CerebrA, registration and manual label correction of Mindboggle-101 atlas for MNI-ICBM152 template
Authors: Manera Ana L. , Dadar Mahsa , Fonov Vladimir , Collins D. Louis 
Published: July 2020

AbstractAccurate anatomical atlases are recognized as important tools in brain-imaging research. They are widely used to estimate disease-specific changes and therefore, are of great relevance in extracting regional information on volumetric variations in clinical cohorts in comparison to healthy populations. The use of high spatial resolution magnetic resonance imaging and the improvement in data preprocessing methods have enabled the study of structural volume changes on a wide range of disorders, particularly in neurodegenerative diseases where different brain morphometry analyses are being broadly used in an effort to improve diagnostic biomarkers. In the present dataset, we introduce the Cerebrum Atlas (CerebrA) along with the MNI-ICBM2009c average template. MNI-ICBM2009c is the most recent version of the MNI-ICBM152 brain average, providing a higher level of anatomical details. Cerebra is based on an accurate non-linear registration of cortical and subcortical labelling from Mindboggle 101 to the symmetric MNI-ICBM2009c atlas, followed by manual editing.
Factor structure of the Edinburgh Postnatal Depression Scale in the Japan Environment and Children’s Study
Authors: Matsumura Kenta , Hamazaki Kei , Tsuchida Akiko , Kasamatsu Haruka , Inadera Hidekuni ,   The Japan Environment and Children’s Study (JECS) Group, Kamijima Michihiro , Yamazaki Shin , Ohya Yukihiro , Kishi Reiko , Yaegashi Nobuo , Hashimoto Koichi , Mori Chisato , Ito Shuichi , Yamagata Zentaro , Nakayama Takeo , Iso Hiroyasu , Shima Masayuki , Kurozawa Youichi , Suganuma Narufumi , Kusuhara Koichi , Katoh Takahiko 
Published: July 2020

AbstractThe Edinburgh Postnatal Depression Scale (EPDS) is frequently used to screen for postpartum depression. However, its factor structure exhibits noticeable inconsistencies between studies. We examined the EPDS at two postpartum time points using a large dataset from outside Western countries. Participants were 91,063 mothers in an ongoing birth cohort of the Japan Environment and Children’s Study. One-, two-, and three-factor structures of the EPDS at 1- and 6-months postpartum were extracted using exploratory factor analysis (EFA) with oblique rotation. Goodness-of-fit indices of extracted factor structures were compared with prior ones by conducting a confirmatory factor analysis (CFA). CFA revealed that a three-factor model extracted from the current EFA—anxiety (items 3, 4, 5, and 6), depression (items 7, 9, and 10), and anhedonia (items 1 and 2)—showed acceptably high goodness-of-fit and invariability across time. These three factors explained about 65% of the total variance with good reliability (all Cronbach’s αs ≥ 0.70). Most three-factor structures (vs. two-) showed higher goodness-of-fit indices. In conclusion, although we only examined the postpartum period, the EPDS likely comprises three dimensions: anxiety, depression, and anhedonia. Our findings raise questions about the one- or two-factor structure of the EPDS.Trial registration: UMIN000030786.
Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies
Authors: Salvà-Serra Francisco , Jaén-Luchoro Daniel , Jakobsson Hedvig E. , Gonzales-Siles Lucia , Karlsson Roger , Busquets Antonio , Gomila Margarita , Bennasar-Figueras Antoni , Russell Julie E. , Fazal Mohammed Abbas , Alexander Sarah , Moore Edward R. B. 
Published: July 2020

AbstractWe present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.
The pharmaceutical solvent N-methyl-2-pyrollidone (NMP) attenuates inflammation through Krüppel-like factor 2 activation to reduce atherogenesis
Authors: Roche-Molina Marta , Hardwick Bryn , Sanchez-Ramos Cristina , Sanz-Rosa David , Gewert Dirk , Cruz Francisco M. , Gonzalez-Guerra Andres , Andres Vicente , Palma Joaquin A. , Ibanez Borja , Mckenzie Grahame , Bernal Juan A. 
Published: July 2020

AbstractN-methyl-2-pyrrolidone (NMP) is a versatile water-miscible polar aprotic solvent. It is used as a drug solubilizer and penetration enhancer in human and animal, yet its bioactivity properties remain elusive. Here, we report that NMP is a bioactive anti-inflammatory compound well tolerated in vivo, that shows efficacy in reducing disease in a mouse model of atherosclerosis. Mechanistically, NMP increases the expression of the transcription factor Kruppel-like factor 2 (KLF2). Monocytes and endothelial cells treated with NMP express increased levels of KLF2, produce less pro-inflammatory cytokines and adhesion molecules. We found that NMP attenuates monocyte adhesion to endothelial cells inflamed with tumor necrosis factor alpha (TNF-α) by reducing expression of adhesion molecules. We further show using KLF2 shRNA that the inhibitory effect of NMP on endothelial inflammation and subsequent monocyte adhesion is KLF2 dependent. Enhancing KLF2 expression and activity improves endothelial function, controls multiple genes critical for inflammation, and prevents atherosclerosis. Our findings demonstrate a consistent effect of NMP upon KLF2 activation and inflammation, biological processes central to atherogenesis. Our data suggest that inclusion of bioactive solvent NMP in pharmaceutical compositions to treat inflammatory disorders might be beneficial and safe, in particular to treat diseases of the vascular system, such as atherosclerosis.