bluuebunny/crossref_metadata_2025 huggingface dataset:
Study of AGN contribution on morphological parameters of their host galaxies
Authors: Getachew-Woreta Tilahun , Pović Mirjana , Masegosa Josefa , Perea Jaime , Beyoro-Amado Zeleke , Márquez Isabel
Published: January 2021

We tested how the AGN contribution (5%–75% of the total flux) may affect different morphological parameters commonly used in galaxy classification. We carried out all analysis at z ∼ 0 and at higher redshifts that correspond to the COSMOS field. Using a local training sample of >2000 visually classified galaxies, we carried out all measurements with and without the central source, and quantified how the contribution of a bright nuclear point source could affect different morphological parameters, such as: Abraham and Concelice-Bershady indices, Gini, Asymmetry, M20 moment of light, and Smoothness. We found that concentration indexes are less sensitive to both redshift and brightness in comparison to the other parameters. We also found that all parameters change significantly with AGN contribution. At z ∼ 0, up to a 10% of AGN contribution the morphological classification will not be significantly affect, but for ⩾ 25% of AGN contribution late-type spirals follow the range of parameters of elliptical galaxies and can therefore be misclassified early types.
AGN, host galaxies, and starbursts
Authors: Väisänen Petri
Published: January 2021

AGN by definition live in galaxies. Despite a long history of studies, there is still much ongoing research into the interplay of the nucleus and the host galaxy, how do they affect each other, how is their evolution intertwined. This review will briefly go over the historical developments behind the current understanding of AGN host galaxies, their types and characteristics. It will discuss the starburst and AGN connection in particular, and how these phenomena may be connected or influence each other by means of e.g. gas flows. Finally, some examples of AGN/starburst evolution studies from SALT and other large telescopes will be presented.
Hosts of jetted narrow-line Seyfert 1 galaxies in near-infrared
Authors: Järvelä Emilia
Published: January 2021

Host galaxy morphology studies of jetted narrow-line Seyfert 1 galaxies (NLS1) are scarce. Although it seems that they are mostly hosted by late-type galaxies the results remain inconclusive, mostly due to the small sample size. Increasing the number of studied sources is crucial to achieve statistically significant results and to establish a preferred host type for jetted NLS1s. To this end we observed the host galaxies of nine NLS1s in near-infrared using NOTCam at the Nordic Optical Telescope. Seven of these sources are jetted based on the 37 GHz observations at Metsähovi Radio Observatory, Finland. To determine the morphological types of the hosts we performed photometric decomposition of the near-infrared images using GALFIT. Here we present the results of the host galaxy modelling, discuss the importance of this study to our understanding of the nature of the diverse NLS1 population, as well as its significance and implications for active galactic nuclei research in general.
The relationship between black hole accretion rate and gas properties at the Bondi radius
Authors: Bu De-Fu
Published: January 2021

The mass accretion rate determines the black hole accretion mode and the corresponding efficiency of active galactic nuclei (AGNs) feedback. In large-scale simulations studying galaxy formation and evolution, the Bondi radius can be at most marginally resolved. In these simulations, the Bondi accretion formula is always used to estimate the black hole accretion rate. The Bondi solution can not represent the real accretion process. We perform 77 simulations with varying density and temperature at Bondi radius. We find a formula to calculate the black hole accretion rate based on gas density and temperature at Bondi radius. We find that the formula can accurately predict the luminosity of observed low-luminosity AGNs. This formula can be used in sub-grid models in large-scale simulations with AGNs feedback.
Feedback and star formation in AGNs
Authors: Ho Luis C.
Published: January 2021

I will describe a series of experiments designed to use measurements of the cold ISM content of quasars to constrain the effectiveness of AGN feedback. I will propose new star formation rate indicators and apply them to constrain the star formation rate in quasars.
The role of AGN in galaxy star formation: A case study of a radio galaxy at z = 2.6
Authors: Man Allison
Published: January 2021

Radio galaxies are ideal sites to scrutinize AGN feedback physics, as they are massive galaxies with jets that interact with the surrounding ISM. I will present a detailed analysis of the recent star formation history and conditions of a starbursting, massive radio galaxy at z = 2.6, PKS 0529-549. In the 8.5-hour VLT/X-Shooter spectrum, we detect unambiguous signatures of stellar photospheric absorption lines originating from OB-stars. Comparison with model spectra shows that more than one burst took place in its recent past: the most recent one at 4 − 7 Myr, and another aged ⩾20 Myr. ALMA observations of the [CI] atomic carbon emission line indicates that it has a low molecular gas fraction (∼13%) and short depletion time (∼40 Myr). Most intriguing is the modest velocity dispersion (⩽50 km/s) of these photospheric lines and the ALMA [CI] cold gas. We attribute its efficient star formation to compressive gas motions, induced by radio jets and/or interaction. Star formation works in concert with the AGN to remove any residual molecular gas and eventually leads to quenching.
The spins of supermassive black holes
Authors: Chary Ranga-Ram
Published: January 2021

We present 1-second cadence, precise optical observations from SOFIA and Palomar of a sample of nearby supermassive black holes. The observations were taken to identify the shortest timescale variability in the nuclear photometry which may be associated with instabilities in the accretion flow in the immediate vicinity of the black hole. The shortest timescale variability, if associated with the radius of the innermost stable circular orbit (ISCO), can then be used to estimate the spin of the black hole. Despite 1% precision photometry, we obtained a non-detection of any significant variability in the nucleus of M32 (Mbh ∼ 2.5 × 106 Mȯ). Given the density of the stellar cusp, this argues for a scenario where 1000 Msun seed black holes formed from the coalescence of less massive black holes, which then accrete the gas produced by stellar interactions/winds. In more luminous systems however, we find a significant deection of variability and present hypotheses to explain the signal and thereby the origin of supermassive black holes.
Supermassive black hole seed formation and the impact on black hole populations across cosmic time
Authors: DeGraf Colin
Published: January 2021

Although it is well understood that supermassive black holes are found in essentially all galaxies, the mechanisms by which they initially form remain highly uncertain, despite the importance that the formation pathway can have on AGN and quasar behaviour at all redshifts. Using a post-processing analysis method combining cosmological simulations and analytic modeling, I will discuss how varying the conditions for formation of supermassive black hole seeds leads to changes in AGN populations. Looking at formation via direct collapse or from PopIII remnants, I will discuss the impact on black hole mass and luminosity functions, scaling relations, and black hole mergers, which each have effects at both high- and low-redshifts. In addition to demonstrating the importance of initial seed formation on our understanding of long-term black hole evolution, I will also show that the signatures of seed formation suggest multiple means by which upcoming electromagnetic and GW surveys (at both high- and low-z) can provide the data required to constrain initial supermassive black hole formation.
Multiwavelength morphological study of active galaxies
Authors: Bilata-Woldeyes Betelehem , Pović Mirjana , Beyoro-Amado Zeleke , Getachew-Woreta Tilahun , Terefe Shimeles
Published: January 2021

Studying the morphology of a large sample of active galaxies at different wavelengths and comparing it with active galactic nuclei (AGN) properties, such as black hole mass (MBH) and Eddington ratio (λEdd), can help us in understanding better the connection between AGN and their host galaxies and the role of nuclear activity in galaxy formation and evolution. By using the BAT-SWIFT hard X-ray public data and by extracting those parameters measured for AGN and by using other public catalogues for parameters such as stellar mass (M*), star formation rate (SFR), bolometric luminosity (Lbol), etc., we studied the multiwavelength morphological properties of host galaxies of ultra-hard X-ray detected AGN and their correlation with other AGN properties. We found that ultra hard X-ray detected AGN can be hosted by all morphological types, but in larger fractions (42%) they seem to be hosted by spirals in optical, to be quiet in radio, and to have compact morphologies in X-rays. When comparing morphologies with other galaxy properties, we found that ultra hard X-ray detected AGN follow previously obtained relations. On the SFR vs. stellar mass diagram, we found that although the majority of sources are located below the main sequence (MS) of star formation (SF), still non-negligible number of sources, with diverse morphologies, is located on and/or above the MS, suggesting that AGN feedback might have more complex influence on the SF in galaxies than simply quenching it, as it was suggested in some of previous studies.
Optical spectroscopy of type-2 LINERs
Authors: Hermosa Muñoz Laura , Cazzoli Sara , Márquez Isabel , Masegosa Josefa
Published: January 2021

Low-Ionisation Nuclear Emission-line Regions (LINERs) are the least luminous and the most numerous among the local population of Active Galactic Nuclei (AGN). They can be classified as type-1 or type-2 if their optical spectra show or do not show, respectively, a broad component. It is associated with the presence of a Broad Line Region (BLR) in these systems. However, recent studies have proven that the classification of type-1 LINERs may be controversial, since space- and ground-based spectroscopy provide contradicting results on the presence of very broad components (Cazzoli et al.2018). We have studied the nuclear spectra of 9 type-2 LINERs with intermediate spectral resolution HST/STIS data. We present the results on our analysis of the different spectral components, and discuss the eventual presence of BLR components in type-2 LINER galaxies, together with the possible presence of outflows, both in comparison with type-1 LINERs. We have found a BLR component in 7 out of the 9 analysed objects within the HST/STIS data.
Jet opening angle and linear scale of launch region of blazars
Authors: Liu Xiang , Jiang Pengfei , Cui Lang
Published: January 2021

We explore the intrinsic jet opening angle (IJOA) of blazars, from the literature, we found that the blazar number density peaks around 0.5° of IJOA and declines quickly with increasing IJOA for flat spectrum radio quasars (FSRQs), while the number density has double peaks around 0.3° and 2.0° of IJOA for BL Lacs. We assume that the black hole accretion-produced jet may have the smaller IJOA (for its larger linear scale of launch region), and the BH spin-produced jet may have the larger IJOA (for its smaller launch region), such that the FSRQs are accretion dominated for their single peaked small IJOA, while the BL Lacs are either accretion or BH spin dominated for their double peaked IJOA.
Catalogue with visual morphological classification of 32,616 radio galaxies with optical hosts
Authors: Żywucka Natalia , Koziel-Wierzbowska Dorota , Goyal Arti
Published: January 2021

We present the catalogue of Radio sources associated with Optical Galaxies and having Unresolved or Extended morphologies I (ROGUE I). It was generated by cross-matching galaxies from the Sloan Digital Sky Survey Data Release 7 (SDSS DR 7) as well as radio sources from the First Images of Radio Sky at Twenty Centimetre (FIRST) and the National Radio Astronomical Observatory VLA Sky Survey (NVSS) catalogues. We created the largest handmade catalogue of visually classified radio objects and associated with them optical host galaxies, containing 32,616 galaxies with a FIRST core within 3 arcsec of the optical position. All listed objects possess the good quality SDSS DR 7 spectra with the signal-to-noise ratio > 10 and spectroscopic redshifts up to z = 0.6. The radio morphology classification was performed by a visual examination of the FIRST and the NVSS contour maps overlaid on a DSS image, while an optical morphology classification was based on the 120 arcsec snapshot images from SDSS DR 7.

The majority of radio galaxies in ROGUE I, i.e. ∼ 93%, are unresolved (compact or elongated), while the rest of them exhibit extended morphologies, such as Fanaroff-Riley (FR) type I, II, and hybrid, wide-angle tail, narrow-angle tail, head-tail sources, and sources with intermittent or reoriented jet activity, i.e. double–double, X–shaped, and Z–shaped. Most of FR IIs have low radio luminosities, comparable to the luminosities of FR Is. Moreover, due to visual check of all radio maps and optical images, we were able to discover or reclassify a number of radio objects as giant, double–double, X–shaped, and Z–shaped radio galaxies. The presented sample can serve as a database for training automatic methods of identification and classification of optical and radio galaxies.
X-ray variability plane revisited: Role of obscuration
Authors: González-Martn Omaira
Published: January 2021

Scaling relations are the most powerful astrophysical tools to set constraints to the physical mechanisms of astronomical sources and to infer properties for objects where they cannot be accessed directly. We have re-investigated one of these scaling relations using powerful type 1 Seyferts; the so-called X-ray variability plane (or mass-luminosity-timescale relation, McHardy et al.2006). This relation links the power-spectral density (PSD) break frequency with the SMBH mass and the bolometric luminosity. We used all available XMM-Newton observations to study the PSD and spectra in short segments within each observation. This allows us to report for the first time that the PSD break frequency varies for each object, showing variations in 19 out of the 22 AGN analyzed. Our analysis of the variability plane confirms the relation between the break frequency and the SMBH mass and finds that the obscuration along the line of sight (or the variations on the obscuration using its standard deviation) is also a required parameter. We constrain a new variability plane of the form: log(vBreak) = – A log (MBH) + B log (NH) – C (or log(vBreak) = – A log (MBH) + B Δ (NH) + C). The X-ray variability plane found by McHardy et al. (2006) is roughly recovered when we use unobscured segments. We speculate the PSD shape is related with the outflowing wind close to the accretion disk at least for these powerful type 1 AGN (Gonzalez-Martin et al. 2018).
The impact of CMEs on the critical frequency of F2-layer ionosphere (foF2)
Authors: Seyoum Alene , Gopalswamy Nat , Nigussie Melessew , Mezgebe Nigusse
Published: January 2021

The ionospheric critical frequency (foF2) from ionosonde measurements at geographic high, middle, and low latitudes are analyzed with the occurrence of coronal mass ejections (CMEs) in long term variability of the solar cycles. We observed trends of monthly maximum foF2 values and monthly averaged values of CME parameters such as speed, angular width, mass, and kinetic energy with respect to time. The impact of CMEs on foF2 is very high at high latitudes and low at low latitudes. The time series for monthly maximum foF2 and monthly-averaged CME speed are moderately correlated at high and middle latitudes.
Electron-proton interaction in radio sources
Authors: Obini Halima Ugomma
Published: January 2021

A method of treating electron-proton interaction is presented. The energies involved in the interaction are estimated. Only elastic collisions are considered. The cross sections of the processes are not taken into account. Calculations are carried out in the centre of mass frame. Relevant quantities are transformed into the laboratory frame. Results indicate that the energy per collision gained by an electron ranges from 0.5 MeV to 0.6 MeV, under suitable conditions.
Floodplain Wetland Channel Planform, Cross‐Sectional Morphology, and Sediment Characteristics Along an Estuarine to Tidal River Gradient
Authors: Diefenderfer Heida L. , Borde Amy B. , Cullinan Valerie I.
Published: January 2021

The formation of wetland channel networks on coastal river floodplains is affected by spatial transitions in tidal‐fluvial processes. This study evaluated sedimentation patterns in tidal marshes on the 147‐km tidal Columbia River and its 87‐km estuary and characterized the cross‐sectional geometry and planform morphometry of tidal wetlands along the estuarine to riverine gradient. Tidal marshes were predominantly depositional (median 0.7 cm yr−1, primarily silt), consistent with late‐Holocene rates. Marsh sediment accretion rate increased with annual maximum 7‐day average daily maximum water depth. Elevation was negatively correlated with accretion rate in the tidal river and positively correlated with total organic carbon (TOC%) in the tidal river and estuary. TOC% was greater in the estuary and, like percent fines, greater farther from the main‐channel Columbia River. For four single‐channel and six channel‐network planforms of tidal marsh, shrub‐dominated, and forested wetlands: (1) Spatial patterns of cross‐sectional morphology conformed to typical coastal wetland morphology in estuarine reaches up to the tidal river. (2) Reach‐based and common slope linear models for channel perimeter on wetland area were predictive in the estuary (R2 > 0.81) and differed between island (n = 144) and mainland (n = 164) wetlands. No planform linear models were predictive for the entire study area or the tidal river. No models for channel outlets were acceptable. (3) Channel perimeter, surface area, and outlets were all highly variable within and among estuarine–riverine reaches. Analyses of sediment, cross‐section, and planform support the use of a “natural network paradigm” for wetland‐restoration design on tidal river floodplains.
Micro/nanodevices for assessment and treatment in stomatology and ophthalmology
Authors: Sheng An’an , Lin Long , Zhu Jia , Zhuang Jian , Li Jian , Chang Lingqian , Cheng Huanyu
Published: January 2021

Micro/nanodevices have been widely applied for the real-time monitoring of intracellular activities and the delivery of exogenous substances in the past few years. This review focuses on miniaturized micro/nanodevices for assessment and treatment in stomatology and ophthalmology. We first summarize the recent progress in this field by examining the available materials and fabrication techniques, device design principles, mechanisms, and biosafety aspects of micro/nanodevices. Following a discussion of biochemical sensing technology from the cellular level to the tissue level for disease assessment, we then summarize the use of microneedles and other micro/nanodevices in the treatment of oral and ocular diseases and conditions, including oral cancer, eye wrinkles, keratitis, and infections. Along with the identified key challenges, this review concludes with future directions as a small fraction of vast opportunities, calling for joint efforts between clinicians and engineers with diverse backgrounds to help facilitate the rapid development of this burgeoning field in stomatology and ophthalmology.
Rosmarinic acid suppresses tau phosphorylation and cognitive decline by downregulating the JNK signaling pathway
Authors: Yamamoto So , Kayama Tomoko , Noguchi-Shinohara Moeko , Hamaguchi Tsuyoshi , Yamada Masahito , Abe Keiko , Kobayashi Shoko
Published: January 2021

Rosmarinic acid (RA), a polyphenol found in Lamiaceae herbs, is a candidate of preventive ingredients against Alzheimer’s disease (AD) as it potently suppresses the aggregation of amyloid β (Aβ); however, the effect of RA on tau phosphorylation and cognitive dysfunction remains unclear. The present study revealed that RA intake inhibited the pathological hallmarks of AD, including Aβ and phosphorylated tau accumulation, and improved cognitive function in the 3 × Tg-AD mouse model. Additionally, RA intake suppressed hippocampal inflammation and led to the downregulation of the JNK signaling pathway that induces tau phosphorylation. Feeding with RA exerted an anti-inflammatory effect not only in the central nervous system but also in the periphery. Downregulation of the JNK signaling pathway in hippocampus may be a potential mechanism underlying the inhibition of progression of pathology and cognitive deficit by RA feeding.
A single-dose live attenuated chimeric vaccine candidate against Zika virus
Authors: Chin Wei-Xin , Lee Regina Ching Hua , Kaur Parveen , Lew Tian Sheng , Yogarajah Thinesshwary , Kong Hao Yuin , Teo Zi-Yun , Salim Cyrill Kafi , Zhang Rong-Rong , Li Xiao-Feng , Alonso Sylvie , Qin Cheng-Feng , Chu Justin Jang Hann
Published: January 2021

The mosquito-borne Zika virus is an emerging pathogen from the Flavivirus genus for which there are no approved antivirals or vaccines. Using the clinically validated PDK-53 dengue virus vaccine strain as a backbone, we created a chimeric dengue/Zika virus, VacDZ, as a live attenuated vaccine candidate against Zika virus. VacDZ demonstrates key markers of attenuation: small plaque phenotype, temperature sensitivity, attenuation of neurovirulence in suckling mice, and attenuation of pathogenicity in interferon deficient adult AG129 mice. VacDZ may be administered as a traditional live virus vaccine, or as a DNA-launched vaccine that produces live VacDZ in vivo after delivery. Both vaccine formulations induce a protective immune response against Zika virus in AG129 mice, which includes neutralising antibodies and a strong Th1 response. This study demonstrates that VacDZ is a safe and effective vaccine candidate against Zika virus.
Synthetic skull bone defects for automatic patient-specific craniofacial implant design
Authors: Li Jianning , Gsaxner Christina , Pepe Antonio , Morais Ana , Alves Victor , von Campe Gord , Wallner Jürgen , Egger Jan
Published: January 2021

Patient-specific craniofacial implants are used to repair skull bone defects after trauma or surgery. Currently, cranial implants are designed and produced by third-party suppliers, which is usually time-consuming and expensive. Recent advances in additive manufacturing made the in-hospital or in-operation-room fabrication of personalized implants feasible. However, the implants are still manufactured by external companies. To facilitate an optimized workflow, fast and automatic implant manufacturing is highly desirable. Data-driven approaches, such as deep learning, show currently great potential towards automatic implant design. However, a considerable amount of data is needed to train such algorithms, which is, especially in the medical domain, often a bottleneck. Therefore, we present CT-imaging data of the craniofacial complex from 24 patients, in which we injected various artificial cranial defects, resulting in 240 data pairs and 240 corresponding implants. Based on this work, automatic implant design and manufacturing processes can be trained. Additionally, the data of this work build a solid base for researchers to work on automatic cranial implant designs.
An exceptionally high wave at the CNR-ISMAR oceanographic tower in the Northern Adriatic Sea
Authors: Cavaleri Luigi , Barbariol Francesco , Bastianini Mauro , Benetazzo Alvise , Bertotti Luciana , Pomaro Angela
Published: January 2021

On December 15, 2009, a very high wave crest was recorded by a local camera at the CNR-ISMAR oceanographic tower, 15 km offshore Venice in the Northern Adriatic Sea (Italy). The height of the estimated crest elevation appears well beyond the value (1,25·Hs) commonly used to identify a wave as freak. We document the wave event with a full description of the corresponding met-ocean conditions and related measurements, of which we provide a critical analysis.
Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera
Authors: Li Hui , Yang Xingyu , Zhang Yue , Gao Zhiyan , Liang Yuting , Chen Jinming , Shi Tao
Published: January 2021

Sacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.
Survival of hypoxia-induced dormancy is not a common feature of all strains of the Mycobacterium tuberculosis complex
Authors: Tizzano Barbara , Dallenga Tobias K. , Utpatel Christian , Behrends Jochen , Homolka Susanne , Kohl Thomas A. , Niemann Stefan
Published: January 2021

While persistence in a dormant state is crucial for the life cycle of Mycobacterium tuberculosis, no investigation regarding dormancy survival of different strains across different lineages was performed so far. We analyzed responses to oxygen starvation and recovery in terms of growth, metabolism, and transcription. All different strains belonging to the Euro-American lineage (L4) showed similar survival and resuscitation characteristics. Different clinical isolates from the Beijing (L2), East African-Indian (L3), and Delhi/Central Asian (L1) lineage did not survive oxygen starvation. We show that dormancy survival is lineage-dependent. Recovery from O2 starvation was only observed in strains belonging to the Euro-American (L4) lineage but not in strains belonging to different lineages (L1, L2, L3). Thus, resuscitation from dormancy after oxygen starvation is not a general feature of all M. tuberculosis strains as thought before. Our findings are of key importance to understand infection dynamics of non-Euro-American vs Euro-American strains and to develop drugs targeting the dormant state.
Non-apoptotic enteroblast-specific role of the initiator caspase Dronc for development and homeostasis of the Drosophila intestine
Authors: Lindblad Jillian L. , Tare Meghana , Amcheslavsky Alla , Shields Alicia , Bergmann Andreas
Published: January 2021

The initiator caspase Dronc is the only CARD-domain containing caspase in Drosophila and is essential for apoptosis. Here, we report that homozygous dronc mutant adult animals are short-lived due to the presence of a poorly developed, defective and leaky intestine. Interestingly, this mutant phenotype can be significantly rescued by enteroblast-specific expression of dronc+ in dronc mutant animals, suggesting that proper Dronc function specifically in enteroblasts, one of four cell types in the intestine, is critical for normal development of the intestine. Furthermore, enteroblast-specific knockdown of dronc in adult intestines triggers hyperplasia and differentiation defects. These enteroblast-specific functions of Dronc do not require the apoptotic pathway and thus occur in a non-apoptotic manner. In summary, we demonstrate that an apoptotic initiator caspase has a very critical non-apoptotic function for normal development and for the control of the cell lineage in the adult midgut and therefore for proper physiology and homeostasis.
Linking the oral microbiome and salivary cytokine abundance to circadian oscillations
Authors: Sarkar Anujit , Kuehl Melanie N. , Alman Amy C. , Burkhardt Brant R.
Published: January 2021

Saliva has immense potential as a diagnostic fluid for identification and monitoring of several systemic diseases. Composition of the microbiome and inflammation has been associated and reflective of oral and overall health. In addition, the relative ease of collection of saliva further strengthens large-scale diagnostic purposes. However, the future clinical utility of saliva cannot be fully determined without a detailed examination of daily fluctuations that may occur within the oral microbiome and inflammation due to circadian rhythm. In this study, we explored the association between the salivary microbiome and the concentration of IL-1β, IL-6 and IL-8 in the saliva of 12 healthy adults over a period of 24 h by studying the 16S rRNA gene followed by negative binomial mixed model regression analysis. To determine the periodicity and oscillation patterns of both the oral microbiome and inflammation (represented by the cytokine levels), two of the twelve subjects were studied for three consecutive days. Our results indicate that the Operational Taxonomic Units (OTUs) belonging to Prevotella, SR1 and Ruminococcaceae are significantly associated to IL-1β while Prevotella and Granulicatella were associated with IL-8. Our findings have also revealed a periodicity of both the oral microbiome (OTUs) and inflammation (cytokine levels) with identifiable patterns between IL-1β and Prevotella, and IL-6 with Prevotella, Neisseria and Porphyromonas. We believe that this study represents the first measure and demonstration of simultaneous periodic fluctuations of cytokine levels and specific populations of the oral microbiome.
Exploring mobility in Italian Neolithic and Copper Age communities
Authors: De Angelis Flavio , Pellegrini Maura , Martínez-Labarga Cristina , Anzivino Laura , Scorrano Gabriele , Brilli Mauro , Giustini Francesca , Angle Micaela , Calattini Mauro , Carboni Giovanni , Catalano Paola , Ceccaroni Emanuela , Cosentino Serena , Di Giannantonio Stefania , Isola Ilaria , Martini Fabio , Pacciani Elsa , Radina Francesca , Rolfo Mario Federico , Silvestrini Mara , Volante Nicoletta , Zanchetta Giovanni , Sarti Lucia , Rickards Olga
Published: January 2021

As a means for investigating human mobility during late the Neolithic to the Copper Age in central and southern Italy, this study presents a novel dataset of enamel oxygen and carbon isotope values (δ18Oca and δ13Cca) from the carbonate fraction of biogenic apatite for one hundred and twenty-six individual teeth coming from two Neolithic and eight Copper Age communities. The measured δ18Oca values suggest a significant role of local sources in the water inputs to the body water, whereas δ13Cca values indicate food resources, principally based on C3 plants. Both δ13Cca and δ18Oca ranges vary substantially when samples are broken down into local populations. Statistically defined thresholds, accounting for intra-site variability, allow the identification of only a few outliers in the eight Copper Age communities, suggesting that sedentary lifestyle rather than extensive mobility characterized the investigated populations. This seems to be also typical of the two studied Neolithic communities. Overall, this research shows that the investigated periods in peninsular Italy differed in mobility pattern from the following Bronze Age communities from more northern areas.
Molecular preservation in mammoth bone and variation based on burial environment
Authors: Colleary Caitlin , Lamadrid Hector M. , O’Reilly Shane S. , Dolocan Andrei , Nesbitt Sterling J.
Published: January 2021

Biomolecules preserved in fossils are expanding our understanding of the biology and evolution of ancient animals. Molecular taphonomy seeks to understand how these biomolecules are preserved and how they can be interpreted. So far, few studies on molecular preservation have considered burial context to understand its impact on preservation or the potentially complementary information from multiple biomolecular classes. Here, we use mass spectrometry and other analytical techniques to detect the remains of proteins and lipids within intact fossil mammoth bones of different ages and varied depositional setting. By combining these approaches, we demonstrate that endogenous amino acids, amides and lipids can preserve well in fossil bone. Additionally, these techniques enable us to examine variation in preservation based on location within the bone, finding dense cortical bone better preserves biomolecules, both by slowing the rate of degradation and limiting the extent of exogenous contamination. Our dataset demonstrates that biomolecule loss begins early, is impacted by burial environment and temperature, and that both exogenous and endogenous molecular signals can be both present and informative in a single fossil.
Spectrum analysis of inborn errors of metabolism for expanded newborn screening in a northwestern Chinese population
Authors: Zhang Ruixue , Qiang Rong , Song Chengrong , Ma Xiaoping , Zhang Yan , Li Fengxia , Wang Rui , Yu Wenwen , Feng Mei , Yang Lihui , Wang Xiaobin , Cai Na
Published: January 2021

Expanded newborn screening facilitates early identification and intervention of patients with inborn errors of metabolism (IEMs), There is a lack of disease spectrum data for many areas in China. To determine the disease spectrum and genetic characteristics of IEMs in Xi'an city of Shaanxi province in northwest China, 146152 newborns were screening by MSMS from January 2014 to December 2019 and 61 patients were referred to genetic analysis by next generation sequencing (NGS) and validated by Sanger sequencing. Seventy-five newborns and two mothers were diagnosed with IEMs, with an overall incidence of 1:1898 (1:1949 without mothers). There were 35 newborns with amino acidemias (45.45%, 1:4176), 28 newborns with organic acidurias (36.36%, 1:5220), and 12 newborns and two mothers with FAO disorders (18.18%; 1:10439 or 1:12179 without mothers). Phenylketonuria and methylmalonic acidemia were the two most common disorders, accounting for 65.33% (49/75) of all confirmed newborn. Some hotspot mutations were observed for several IEMs, including PAH gene c.728G>A for phenylketonuria; MMACHC gene c.609G>A and c.567dupT, MMUT gene c.323G>A for methylmalonic acidemia and SLC25A13 gene c.852_855del for citrin deficiency. Our study provides effective clinical guidance for the popularization and application of expanded newborn screening, genetic screening, and genetic counseling of IEMs in this region.
F/OH ratio in a rare fluorine-poor blue topaz from Padre Paraíso (Minas Gerais, Brazil) to unravel topaz’s ambient of formation
Authors: Precisvalle N. , Martucci A. , Gigli L. , Plaisier J. R. , Hansen T. C. , Nobre A. G. , Bonadiman C.
Published: January 2021

Topaz [Al2SiO4(F,OH)2] is one of the main fluorine-bearing silicates occurring in environments where variably acidic (F)/aqueous (OH) fluids saturate the silicate system. In this work we fully characterized blue topaz from Padre Paraíso (Minas Gerais, Brazil) by means of in situ synchrotron X-Ray and neutron powder diffraction measurements (temperature range 298–1273 K) combined with EDS microanalyses. Understanding the role of OH/F substitution in topaz is important in order to determine the hydrophilicity and the exchange reactions of fluorine by hydroxyl groups, and ultimately to characterize the environmental redox conditions (H2O/F) required for mineral formation. The fluorine content estimated from neutron diffraction data is ~ 1.03 a.f.u (10.34 wt%), in agreement with the chemical data (on average 10.0 wt%). The XOH [OH/(OH + F)] (0.484) is close to the maximum XOH value (0.5), and represents the OH- richest topaz composition so far analysed in the Minas Gerais district. Topaz crystallinity and fluorine content sharply decrease at 1170 K, while mullite phase starts growing. On the basis of this behaviour, we suggest that this temperature may represent the potential initial topaz’s crystallization temperature from supercritical fluids in a pegmatite system. The log(fH2O/fHF)fluid (1.27 (0.06)) is coherent with the fluorine activity calculated for hydrothermal fluids (pegmatitic stage) in equilibrium with the forming mineral (log(fH2O/fHF)fluid = 1.2–6.5) and clearly different from pure magmatic (granitic) residual melts [log(fH2O/fHF)fluid < 1]. The modelled H2O saturated fluids with the F content not exceeding 1 wt% may represent an anomalous water-dominant / fluorine-poor pegmatite lens of the Padre Paraíso Pegmatite Field.
Effects of integrated biocontrol on bacterial wilt and rhizosphere bacterial community of tobacco
Authors: Hu Yun , Li Yanyan , Yang Xiaoqiong , Li Chunli , Wang Lin , Feng Ji , Chen Shouwen , Li Xihong , Yang Yong
Published: January 2021

Bacterial wilt as a soil-borne disease was caused byRalstonia solanacearum, and seriously damages the growth of tobacco. Integrated biocontrol method was explored to control bacterial wilt. Nevertheless, the long-term effects of the integrated biocontrol method on soil bacterial community, soil physicochemical properties and the incidence of bacterial wilt are not well understood. In this study,B. amyoliquefaciensZM9, calcium cyanamide and rice bran were applied to tobacco fields in different ways. The disease index and incidence of tobacco bacterial wilt (TBW), soil physicochemical properties, colonization ability ofB. amyoliquefaciensZM9, and rhizopshere bacterial community were investigated. The results showed that the integrated application ofB. amyoliquefaciensZM9, rice bran and calcium cyanamide had the highest control efficiency of TBW and bacteria community diversity. Additionally, the integrated biocontrol method could improve the colonization ability ofB. amyoliquefaciensZM9. Furthermore, the integrated biocontrol method could effectively suppress TBW by regulating soil physicochemical properties, promoting beneficial bacteria and antagonistic bacteria of rhizopshere soil. This strategy has prospect of overcoming the defects in application of a single antagonistic bacteria and provides new insights to understand how to improve the colonization capacity of antagonistic bacteria and control efficacy for TBW.
Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front
Authors: Ramond Pierre , Siano Raffaele , Schmitt Sophie , de Vargas Colomban , Marié Louis , Memery Laurent , Sourisseau Marc
Published: January 2021

Oceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample. However, an increasing number of theoretical approaches hypothesize that these processes affect phytoplankton diversity which have cascading effects on regional ecosystems. In 2015, we targeted the Iroise Sea (France) and evidenced the setting up of the Ushant tidal front from the beginning of spring to late summer. Seawater samples were taken during three sampling cruises and DNA-barcoding allowed us to investigate patterns of eukaryotic phytoplankton diversity across this front. First focusing on patterns of taxonomic richness, we evidenced that the front harbored a hotspot of eukaryotic phytoplankton diversity sustained throughout summer. We then detail the ecological processes leading to the formation of this hotspot by studying shifts in community composition across the Iroise Sea. Physical mixing mingled the communities surrounding the front, allowing the formation of a local ecotone, but it was cycles of disturbances and nutrient inputs over the front that allowed a decrease in competitive exclusion, which maintained a higher diversity of rare phytoplankton taxa. These processes did not select a specific ecological strategy as inferred by a trait approach coupled to our taxonomic approach. Instead the front favored higher richness within widespread strategies, resulting in functional redundancy. We detail how fine-scale ocean physics affect phytoplankton diversity and suppose that this interplay is a major control on regional ecosystems.
Multiparametric ultrasound imaging for the assessment of normal versus steatotic livers
Authors: Basavarajappa Lokesh , Baek Jihye , Reddy Shreya , Song Jane , Tai Haowei , Rijal Girdhari , Parker Kevin J. , Hoyt Kenneth
Published: January 2021

Liver disease is increasing in prevalence across the globe. We present here a multiparametric ultrasound (mpUS) imaging approach for assessing nonalcoholic fatty liver disease (NALFD). This study was performed using rats (N = 21) that were fed either a control or methionine and choline deficient (MCD) diet. A mpUS imaging approach that includes H-scan ultrasound (US), shear wave elastography, and contrast-enhanced US measurements were then performed at 0 (baseline), 2, and 6 weeks. Thereafter, animals were euthanized and livers excised for histological processing. A support vector machine (SVM) was used to find a decision plane that classifies normal and fatty liver conditions. In vivo mpUS results from control and MCD diet fed animals reveal that all mpUS measures were different at week 6 (P < 0.05). Principal component analysis (PCA) showed that the H-scan US data contributed the highest percentage to the classification among the mpUS measurements. The SVM resulted in 100% accuracy for classification of normal and high fat livers and 92% accuracy for classification of normal, low fat, and high fat livers. Histology findings found considerable steatosis in the MCD diet fed animals. This study suggests that mpUS examinations have the potential to provide a comprehensive estimation of the main components of early stage NAFLD.
Deep COVID DeteCT: an international experience on COVID-19 lung detection and prognosis using chest CT
Authors: Lee Edward H. , Zheng Jimmy , Colak Errol , Mohammadzadeh Maryam , Houshmand Golnaz , Bevins Nicholas , Kitamura Felipe , Altinmakas Emre , Reis Eduardo Pontes , Kim Jae-Kwang , Klochko Chad , Han Michelle , Moradian Sadegh , Mohammadzadeh Ali , Sharifian Hashem , Hashemi Hassan , Firouznia Kavous , Ghanaati Hossien , Gity Masoumeh , Doğan Hakan , Salehinejad Hojjat , Alves Henrique , Seekins Jayne , Abdala Nitamar , Atasoy Çetin , Pouraliakbar Hamidreza , Maleki Majid , Wong S. Simon , Yeom Kristen W.
Published: January 2021

The Coronavirus disease 2019 (COVID-19) presents open questions in how we clinically diagnose and assess disease course. Recently, chest computed tomography (CT) has shown utility for COVID-19 diagnosis. In this study, we developed Deep COVID DeteCT (DCD), a deep learning convolutional neural network (CNN) that uses the entire chest CT volume to automatically predict COVID-19 (COVID+) from non-COVID-19 (COVID−) pneumonia and normal controls. We discuss training strategies and differences in performance across 13 international institutions and 8 countries. The inclusion of non-China sites in training significantly improved classification performance with area under the curve (AUCs) and accuracies above 0.8 on most test sites. Furthermore, using available follow-up scans, we investigate methods to track patient disease course and predict prognosis.
Algorithmic matching of personal protective equipment donations with healthcare facilities during the COVID-19 pandemic
Authors: Bala Ram , Lee Charlotte , Pallant Benjamin , Srinivasan Maahika , Lurie Daniel , Jacob Rohit , Bhagchandani Neeraj , Ranney Megan , He Shuhan
Published: January 2021

GetUsPPE.org has built a centralized platform to facilitate matches for PPE donations, with an active role in matching donors with the appropriate recipients. A manual match process was limited by volunteer hours, thus we developed an open-access matching algorithm using a linear programming-based transportation model. From April 14, 2020 to April 27, 2020, the algorithm was used to match 83,136 items of PPE to 135 healthcare facilities in need across the United States with a median of 214.3 miles traveled, 100% of available donations matched, met the full quantity of requested PPE for 67% of recipients matched, and with 46% matches under 30 miles traveled. Compared with the period April 1, 2020 to April 13, 2020, when PPE matching was manual, the algorithm resulted in a 280% increase in matches/day. This publicly available automated algorithm could be deployed in future situations when the healthcare supply chain is insufficient.
Comparative multi-omics analyses reveal differential expression of key genes relevant for parasitism between non-encapsulated and encapsulated Trichinella
Authors: Liu Xiaolei , Feng Yayan , Bai Xue , Wang Xuelin , Qin Rui , Tang Bin , Yu Xinxin , Yang Yong , Liu Mingyuan , Gao Fei
Published: January 2021

Genome assemblies provide a powerful basis of comparative multi-omics analyses that offer insight into parasite pathogenicity, host-parasite interactions, and invasion biology. As a unique intracellular nematode, Trichinella consists of two clades, encapsulated and non-encapsulated. Genomic correlation of the distinct differences between the two clades is still unclear. Here, we report an annotated draft reference genome of non-encapsulated Trichinella, T. pseudospiralis, and perform comparative multi-omics analyses with encapsulated T. spiralis. Genome and methylome analyses indicate that, during Trichinella evolution, the two clades of Trichinella exhibit differential expansion and methylation of parasitism-related multi-copy gene families, especially for the DNase II members of the phospholipase D superfamily and Glutathione S-transferases. Further, methylome and transcriptome analyses revealed divergent key excretory/secretory (E/S) genes between the two clades. Among these key E/S genes, TP12446 is significantly more expressed across three life stages in T. pseudospiralis. Overexpression of TP12446 in the mouse C2C12 skeletal muscle cell line could induce inhibition of myotube formation and differentiation, further indicating its key role in parasitism of T. pseudospiralis. This multi-omics study provides a foundation for further elucidation of the mechanism of nurse cell formation and immunoevasion, as well as the identification of pharmacological and diagnostic targets of trichinellosis.
Dipeptidyl peptidase 4 promotes peritoneal fibrosis and its inhibitions prevent failure of peritoneal dialysis
Authors: Li Yi-Chen , Sung Pei-Hsun , Yang Yao-Hsu , Chiang John Y. , Yip Hon-Kan , Yang Chih‐Chao
Published: January 2021

Peritoneal dialysis (PD) possesses multiple advantages for end stage renal disease. However, long-term PD triggers peritoneal fibrosis (PF). From the nationwide analysis of diabetic PD patients (n = 19,828), we identified the incidence of PD failure was significantly lower in diabetic patients treated with dipeptidyl peptidase 4 (DPP4) inhibitors. Experimental study further showed high concentration of glucose remarkably enhanced DPP4 to promote epithelial-mesenchymal transition (EMT) in the mesothelial cells. In chlorhexidine gluconate (CG)-induced PF model of rats, DPP4 expression was enriched at thickening peritoneum. Moreover, as to CG-induced PF model, DPP4 deficiency (F344/DuCrlCrlj strain), sitagliptin and exendin-4 treatments significantly inhibited DPP4 to reverse the EMT process, angiogenesis, oxidative stress, and inflammation, resulting in the protection from PF, preservation of peritoneum and the corresponding functional integrity. Furthermore, DPP4 activity was significantly correlated with peritoneal dysfunction. Taken together, DPP4 caused peritoneal dysfunction/PF, whereas inhibition of DPP4 protected the PD patients against PD failure.