bluuebunny/crossref_metadata_2025 huggingface dataset:
Silicon Isotopes in an EMIC's Ocean: Sensitivity to Runoff, Iron Supply, and Climate
Authors: Dietze H. , Löptien U. , Hordoir R. , Heinemann M. , Huiskamp W. , Schneider B.
Published: September 2020

The isotopic composition of Si in biogenic silica (BSi), such as opal buried in the oceans' sediments, has changed over time. Paleorecords suggest that the isotopic composition, described in terms of δ30Si, was generally much lower during glacial times than today. There is consensus that this variability is attributable to differing environmental conditions at the respective time of BSi production and sedimentation. The detailed links between environmental conditions and the isotopic composition of BSi in the sediments remain, however, poorly constrained. In this study, we explore the effects of a suite of offset boundary conditions during the Last Glacial Maximum (LGM) on the isotopic composition of BSi archived in sediments in an Earth System Model of intermediate complexity (EMIC). Our model results suggest that a change in the isotopic composition of Si supply to the glacial ocean is sufficient to explain the observed overall low(er) glacial δ30Si in BSi. All other processes explored trigger model responses of either wrong sign or magnitude or are inconsistent with a recent estimate of bottom water oxygenation in the Atlantic Sector of the Southern Ocean. Caveats, mainly associated with generic uncertainties in today's pelagic biogeochemical modules, remain.
Brain tumor diagnostic model and dietary effect based on extracellular vesicle microbiome data in serum
Authors: Yang Jinho , Moon Hyo Eun , Park Hyung Woo , McDowell Andrea , Shin Tae-Seop , Jee Young-Koo , Kym Sungmin , Paek Sun Ha , Kim Yoon-Keun
Published: September 2020

The human microbiome has been recently associated with human health and disease. Brain tumors (BTs) are a particularly difficult condition to directly link to the microbiome, as microorganisms cannot generally cross the blood–brain barrier (BBB). However, some nanosized extracellular vesicles (EVs) released from microorganisms can cross the BBB and enter the brain. Therefore, we conducted metagenomic analysis of microbial EVs in both serum (152 BT patients and 198 healthy controls (HC)) and brain tissue (5 BT patients and 5 HC) samples based on the V3–V4 regions of 16S rDNA. We then developed diagnostic models through logistic regression and machine learning algorithms using serum EV metagenomic data to assess the ability of various dietary supplements to reduce BT risk in vivo. Models incorporating the stepwise method and the linear discriminant analysis effect size (LEfSe) method yielded 12 and 29 significant genera as potential biomarkers, respectively. Models using the selected biomarkers yielded areas under the curves (AUCs) >0.93, and the model using machine learning resulted in an AUC of 0.99. In addition, Dialister and [Eubacterium] rectale were significantly lower in both blood and tissue samples of BT patients than in those of HCs. In vivo tests showed that BT risk was decreased through the addition of sorghum, brown rice oil, and garlic but conversely increased by the addition of bellflower and pear. In conclusion, serum EV metagenomics shows promise as a rich data source for highly accurate detection of BT risk, and several foods have potential for mitigating BT risk.
Perovskite light-emitting/detecting bifunctional fibres for wearable LiFi communication
Authors: Shan Qingsong , Wei Changting , Jiang Yan , Song Jizhong , Zou Yousheng , Xu Leimeng , Fang Tao , Wang Tiantian , Dong Yuhui , Liu Jiaxin , Han Boning , Zhang Fengjuan , Chen Jiawei , Wang Yongjin , Zeng Haibo
Published: September 2020

Light fidelity (LiFi), which is emerging as a compelling technology paradigm shifting the common means of high-capacity wireless communication technologies, requires wearable and full-duplex compact design because of its great significance in smart wearables as well as the ‘Internet of Things’. However, the construction of the key component of wearable full-duplex LiFi, light-emitting/detecting bifunctional fibres, is still challenging because of the conflicting process between carrier separation and recombination, as well as the highly dynamic film-forming process. Here, we demonstrate light-emitting/detecting bifunctional fibres enabled by perovskite QDs with hybrid components. The hybrid perovskite inks endow fibres with super-smooth QD films. This, combined with the small exciton binding energy and high carrier mobility of perovskite QDs, enables successful integration of electroluminescence and photodetection into monofilaments. The bifunctional fibres possess the narrowest electroluminescence full width at half maximum of ~19 nm and, more importantly, the capability for simultaneously transmitting and receiving information. The successful fabrication of narrow emission full-duplex LiFi fibres paves the way for the fabrication and integration of low crosstalk interoperable smart wearables.
Carbamylated erythropoietin regulates immune responses and promotes long-term kidney allograft survival through activation of PI3K/AKT signaling
Authors: Na Ning , Zhao Daqiang , Zhang Jinhua , Wu Jiaqing , Miao Bin , Li Heng , Luo Yingxun , Tang Zuofu , Zhang Wensheng , Bellanti Joseph A. , Zheng Song Guo
Published: September 2020

Modulation of alloimmune responses is critical to improving transplant outcome and promoting long-term graft survival. To determine mechanisms by which a nonhematopoietic erythropoietin (EPO) derivative, carbamylated EPO (CEPO), regulates innate and adaptive immune cells and affects renal allograft survival, we utilized a rat model of fully MHC-mismatched kidney transplantation. CEPO administration markedly extended the survival time of kidney allografts compared with the transplant alone control group. This therapeutic effect was inhibited when the recipients were given LY294002, a selective inhibitor of the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway or anti-EPO receptor (EPOR) antibody, in addition to CEPO. In vitro, CEPO inhibited the differentiation and function of dendritic cells and modulated their production of pro-inflammatory and anti-inflammatory cytokines, along with activating the PI3K/AKT signaling pathway and increasing EPOR mRNA and protein expression by these innate immune cells. Moreover, after CD4+ T cells were exposed to CEPO the Th1/Th2 ratio decreased and the regulatory T cell (Treg)/Th17 ratio increased. These effects were abolished by LY294002 or anti-EPOR antibody, suggesting that CEPO regulates immune responses and promotes kidney allograft survival by activating the PI3K/AKT signaling pathway in an EPOR-dependent manner. The immunomodulatory and specific signaling pathway effects of CEPO identified in this study suggest a potential therapeutic approach to promoting kidney transplant survival.
Glioma-initiating cells at tumor edge gain signals from tumor core cells to promote their malignancy
Authors: Bastola Soniya , Pavlyukov Marat S. , Yamashita Daisuke , Ghosh Sadashib , Cho Heejin , Kagaya Noritaka , Zhang Zhuo , Minata Mutsuko , Lee Yeri , Sadahiro Hirokazu , Yamaguchi Shinobu , Komarova Svetlana , Yang Eddy , Markert James , Nabors Louis B. , Bhat Krishna , Lee James , Chen Qin , Crossman David K. , Shin-Ya Kazuo , Nam Do-Hyun , Nakano Ichiro
Published: September 2020

Intratumor spatial heterogeneity facilitates therapeutic resistance in glioblastoma (GBM). Nonetheless, understanding of GBM heterogeneity is largely limited to the surgically resectable tumor core lesion while the seeds for recurrence reside in the unresectable tumor edge. In this study, stratification of GBM to core and edge demonstrates clinically relevant surgical sequelae. We establish regionally derived models of GBM edge and core that retain their spatial identity in a cell autonomous manner. Upon xenotransplantation, edge-derived cells show a higher capacity for infiltrative growth, while core cells demonstrate core lesions with greater therapy resistance. Investigation of intercellular signaling between these two tumor populations uncovers the paracrine crosstalk from tumor core that promotes malignancy and therapy resistance of edge cells. These phenotypic alterations are initiated by HDAC1 in GBM core cells which subsequently affect edge cells by secreting the soluble form of CD109 protein. Our data reveal the role of intracellular communication between regionally different populations of GBM cells in tumor recurrence.
Period multiplication cascade at the order-by-disorder transition in uniaxial random field XY magnets
Authors: Basak S. , Dahmen K. A. , Carlson E. W.
Published: September 2020

Uniaxial random field disorder induces a spontaneous transverse magnetization in the XY model. Adding a rotating driving field, we find a critical point attached to the number of driving cycles needed to complete a limit cycle, the first discovery of this phenomenon in a magnetic system. Near the critical drive, time crystal behavior emerges, in which the period of the limit cycles becomes an integer n > 1 multiple of the driving period. The period n can be engineered via specific disorder patterns. Because n generically increases with system size, the resulting period multiplication cascade is reminiscent of that occurring in amorphous solids subject to oscillatory shear near the onset of plastic deformation, and of the period bifurcation cascade near the onset of chaos in nonlinear systems, suggesting it is part of a larger class of phenomena in transitions of dynamical systems. Applications include magnets, electron nematics, and quantum gases.
Deregulated immune cell recruitment orchestrated by FOXM1 impairs human diabetic wound healing
Authors: Sawaya Andrew P. , Stone Rivka C. , Brooks Stephen R. , Pastar Irena , Jozic Ivan , Hasneen Kowser , O’Neill Katelyn , Mehdizadeh Spencer , Head Cheyanne R. , Strbo Natasa , Morasso Maria I. , Tomic-Canic Marjana
Published: September 2020

Diabetic foot ulcers (DFUs) are a life-threatening disease that often result in lower limb amputations and a shortened lifespan. However, molecular mechanisms contributing to the pathogenesis of DFUs remain poorly understood. We use next-generation sequencing to generate a human dataset of pathogenic DFUs to compare to transcriptional profiles of human skin and oral acute wounds, oral as a model of “ideal” adult tissue repair due to accelerated closure without scarring. Here we identify major transcriptional networks deregulated in DFUs that result in decreased neutrophils and macrophages recruitment and overall poorly controlled inflammatory response. Transcription factors FOXM1 and STAT3, which function to activate and promote survival of immune cells, are inhibited in DFUs. Moreover, inhibition of FOXM1 in diabetic mouse models (STZ-induced and db/db) results in delayed wound healing and decreased neutrophil and macrophage recruitment in diabetic wounds in vivo. Our data underscore the role of a perturbed, ineffective inflammatory response as a major contributor to the pathogenesis of DFUs, which is facilitated by FOXM1-mediated deregulation of recruitment of neutrophils and macrophages, revealing a potential therapeutic strategy.
Potential impacts of mercury released from thawing permafrost
Authors: Schaefer Kevin , Elshorbany Yasin , Jafarov Elchin , Schuster Paul F. , Striegl Robert G. , Wickland Kimberly P. , Sunderland Elsie M.
Published: September 2020

Mercury (Hg) is a naturally occurring element that bonds with organic matter and, when converted to methylmercury, is a potent neurotoxicant. Here we estimate potential future releases of Hg from thawing permafrost for low and high greenhouse gas emissions scenarios using a mechanistic model. By 2200, the high emissions scenario shows annual permafrost Hg emissions to the atmosphere comparable to current global anthropogenic emissions. By 2100, simulated Hg concentrations in the Yukon River increase by 14% for the low emissions scenario, but double for the high emissions scenario. Fish Hg concentrations do not exceed United States Environmental Protection Agency guidelines for the low emissions scenario by 2300, but for the high emissions scenario, fish in the Yukon River exceed EPA guidelines by 2050. Our results indicate minimal impacts to Hg concentrations in water and fish for the low emissions scenario and high impacts for the high emissions scenario.
Structural lubricity in soft and hard matter systems
Authors: Vanossi Andrea , Bechinger Clemens , Urbakh Michael
Published: September 2020

Over the recent decades there has been tremendous progress in understanding and controlling friction between surfaces in relative motion. However the complex nature of the involved processes has forced most of this work to be of rather empirical nature. Two very distinctive physical systems, hard two-dimensional layered materials and soft microscopic systems, such as optically or topographically trapped colloids, have recently opened novel rationally designed lines of research in the field of tribology, leading to a number of new discoveries. Here, we provide an overview of these emerging directions of research, and discuss how the interplay between hard and soft matter promotes our understanding of frictional phenomena.
Phase of firing coding of learning variables across the fronto-striatal network during feature-based learning
Authors: Voloh Benjamin , Oemisch Mariann , Womelsdorf Thilo
Published: September 2020

The prefrontal cortex and striatum form a recurrent network whose spiking activity encodes multiple types of learning-relevant information. This spike-encoded information is evident in average firing rates, but finer temporal coding might allow multiplexing and enhanced readout across the connected network. We tested this hypothesis in the fronto-striatal network of nonhuman primates during reversal learning of feature values. We found that populations of neurons encoding choice outcomes, outcome prediction errors, and outcome history in their firing rates also carry significant information in their phase-of-firing at a 10–25 Hz band-limited beta frequency at which they synchronize across lateral prefrontal cortex, anterior cingulate cortex and anterior striatum when outcomes were processed. The phase-of-firing code exceeds information that can be obtained from firing rates alone and is evident for inter-areal connections between anterior cingulate cortex, lateral prefrontal cortex and anterior striatum. For the majority of connections, the phase-of-firing information gain is maximal at phases of the beta cycle that were offset from the preferred spiking phase of neurons. Taken together, these findings document enhanced information of three important learning variables at specific phases of firing in the beta cycle at an inter-areally shared beta oscillation frequency during goal-directed behavior.
Epidemiological and phylogenetic analysis reveals Flavobacteriaceae as potential ancestral source of tigecycline resistance gene tet(X)
Authors: Zhang Rong , Dong Ning , Shen Zhangqi , Zeng Yu , Lu Jiauyue , Liu Congcong , Zhou Hongwei , Hu Yanyan , Sun Qiaoling , Cheng Qipeng , Shu Lingbing , Cai Jiachang , Chan Edward Wai-Chi , Chen Gongxiang , Chen Sheng
Published: September 2020

Emergence of tigecycline-resistance tet(X) gene orthologues rendered tigecycline ineffective as last-resort antibiotic. To understand the potential origin and transmission mechanisms of these genes, we survey the prevalence of tet(X) and its orthologues in 2997 clinical E. coli and K. pneumoniae isolates collected nationwide in China with results showing very low prevalence on these two types of strains, 0.32% and 0%, respectively. Further surveillance of tet(X) orthologues in 3692 different clinical Gram-negative bacterial strains collected during 1994–2019 in hospitals in Zhejiang province, China reveals 106 (2.7%) tet(X)-bearing strains with Flavobacteriaceae being the dominant (97/376, 25.8%) bacteria. In addition, tet(X)s are found to be predominantly located on the chromosomes of Flavobacteriaceae and share similar GC-content as Flavobacteriaceae. It also further evolves into different orthologues and transmits among different species. Data from this work suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance gene tet(X).
Haploinsufficiency of RREB1 causes a Noonan-like RASopathy via epigenetic reprogramming of RAS-MAPK pathway genes
Authors: Kent Oliver A. , Saha Manipa , Coyaud Etienne , Burston Helen E. , Law Napoleon , Dadson Keith , Chen Sujun , Laurent Estelle M. , St-Germain Jonathan , Sun Ren X. , Matsumoto Yoshinori , Cowen Justin , Montgomery-Song Aaryn , Brown Kevin R. , Ishak Charles , Rose Jose La , De Carvalho Daniel D. , He Housheng Hansen , Raught Brian , Billia Filio , Kannu Peter , Rottapel Robert
Published: September 2020

RAS-MAPK signaling mediates processes critical to normal development including cell proliferation, survival, and differentiation. Germline mutation of RAS-MAPK genes lead to the Noonan-spectrum of syndromes. Here, we present a patient affected by a 6p-interstitial microdeletion with unknown underlying molecular etiology. Examination of 6p-interstitial microdeletion cases reveals shared clinical features consistent with Noonan-spectrum disorders including short stature, facial dysmorphia and cardiovascular abnormalities. We find the RAS-responsive element binding protein-1 (RREB1) is the common deleted gene in multiple 6p-interstitial microdeletion cases. Rreb1 hemizygous mice display orbital hypertelorism and cardiac hypertrophy phenocopying the human syndrome. Rreb1 haploinsufficiency leads to sensitization of MAPK signaling. Rreb1 recruits Sin3a and Kdm1a to control H3K4 methylation at MAPK pathway gene promoters. Haploinsufficiency of SIN3A and mutations in KDM1A cause syndromes similar to RREB1 haploinsufficiency suggesting genetic perturbation of the RREB1-SIN3A-KDM1A complex represents a new category of RASopathy-like syndromes arising through epigenetic reprogramming of MAPK pathway genes.
Ultralong purely organic aqueous phosphorescence supramolecular polymer for targeted tumor cell imaging
Authors: Zhou Wei-Lei , Chen Yong , Yu Qilin , Zhang Haoyang , Liu Zhi-Xue , Dai Xian-Yin , Li Jing-Jing , Liu Yu
Published: September 2020

Purely organic room-temperature phosphorescence has attracted attention for bioimaging but can be quenched in aqueous systems. Here we report a water-soluble ultralong organic room-temperature phosphorescent supramolecular polymer by combining cucurbit[n]uril (CB[7], CB[8]) and hyaluronic acid (HA) as a tumor-targeting ligand conjugated to a 4-(4-bromophenyl)pyridin-1-ium bromide (BrBP) phosphor. The result shows that CB[7] mediated pseudorotaxane polymer CB[7]/HA–BrBP changes from small spherical aggregates to a linear array, whereas complexation with CB[8] results in biaxial pseudorotaxane polymer CB[8]/HA–BrBP which transforms to relatively large aggregates. Owing to the more stable 1:2 inclusion complex between CB[8] and BrBP and the multiple hydrogen bonds, this supramolecular polymer has ultralong purely organic RTP lifetime in water up to 4.33 ms with a quantum yield of 7.58%. Benefiting from the targeting property of HA, this supramolecular polymer is successfully applied for cancer cell targeted phosphorescence imaging of mitochondria.
Author Correction: Targeting QKI-7 in vivo restores endothelial cell function in diabetes
Authors: Yang Chunbo , Eleftheriadou Magdalini , Kelaini Sophia , Morrison Thomas , González Marta Vilà , Caines Rachel , Edwards Nicola , Yacoub Andrew , Edgar Kevin , Moez Arya , Ivetic Aleksandar , Zampetaki Anna , Zeng Lingfang , Wilkinson Fiona L. , Lois Noemi , Stitt Alan W. , Grieve David J. , Margariti Andriana
Published: September 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Aberrant electronic and structural alterations in pressure tuned perovskite NaOsO3
Authors: Sereika Raimundas , Liu Peitao , Kim Bongjae , Kim Sooran , Zhang Jianbo , Chen Bijuan , Yamaura Kazunari , Park Changyong , Franchini Cesare , Ding Yang , Mao Ho-kwang
Published: September 2020

The perovskite NaOsO3 has a metal–insulator transition at temperature 410 K, which is delicate, intriguing, and provokes a lot of debate on its nature. Our combined electrical resistance, Raman, and synchrotron x-ray diffraction experiments show that the insulating ground state in this osmate endures under high pressure up to at least 35 GPa. In this pressure range, compression reveals hidden hysteretic resistance properties with a transient metallic state near 200 K, manifested three electronic character anomalies (at 1.7, 9.0, and 25.5 GPa), and a structural transition to the singular polar phase (at ~18 GPa). We distinguish NaOsO3 from the regular crystallographic behavior of perovskites, though the electrical specificities resemble iridates and nickelates. The theoretical first-principle band structure and lattice dynamics calculations demonstrate that the magnetically itinerant Lifshitz-type mechanism with spin–orbit and spin–phonon interactions is responsible for these pressure-induced changes. Our findings provide another new playground for the emergence of new states in 5d materials by using high-pressure methods.
Mechanisms of indigo naturalis on treating ulcerative colitis explored by GEO gene chips combined with network pharmacology and molecular docking
Authors: Gu Sizhen , Xue Yan , Gao Yang , Shen Shuyang , Zhang Yuli , Chen Kanjun , Xue Shigui , Pan Ji , Tang Yini , Zhu Hui , Wu Huan , Dou Danbo
Published: September 2020

Oral administration of indigo naturalis (IN) can induce remission in ulcerative colitis (UC); however, the underlying mechanism remains unknown. The main active components and targets of IN were obtained by searching three traditional Chinese medicine network databases such as TCMSP and five Targets fishing databases such as PharmMapper. UC disease targets were obtained from three disease databases such as DrugBank,combined with four GEO gene chips. IN-UC targets were identified by matching the two. A protein–protein interaction network was constructed, and the core targets were screened according to the topological structure. GO and KEGG enrichment analysis and bioGPS localization were performed,and an Herbs-Components-Targets network, a Compound Targets-Organs location network, and a Core Targets-Signal Pathways network were established. Molecular docking technology was used to verify the main compounds-targets. Ten core active components and 184 compound targets of IN-UC, of which 43 were core targets, were enriched and analyzed by bioGPS, GO, and KEGG. The therapeutic effect of IN on UC may involve activation of systemic immunity, which is involved in the regulation of nuclear transcription, protein phosphorylation, cytokine activity, reactive oxygen metabolism, epithelial cell proliferation, and cell apoptosis through Th17 cell differentiation, the Jak-STAT and IL-17 signaling pathways, toll-like and NOD-like receptors, and other cellular and innate immune signaling pathways. The molecular mechanism underlying the effect of IN on inducing UC remission was predicted using a network pharmacology method, thereby providing a theoretical basis for further study of the effective components and mechanism of IN in the treatment of UC.
Climatic variability at Gangtok and Tadong weather observatories in Sikkim, India, during 1961–2017
Authors: Kumar Parvendra , Sharma Milap Chand , Saini Rakesh , Singh Girish Kumar
Published: September 2020

The present study documents the long-term trends in the temperature and precipitation of a poorly represented region, the Sikkim, eastern Himalaya using the Mann–Kendall non-parametric test and the Sen’s slope estimator. Additionally, the normal distribution curves and Cusum charts have been used to identify the shifts in extreme events and to detect the points of change in the climatic data series for robust analysis. The minimum temperatures recorded a positive trend in Gangtok (0.036 ˚C year−1 from 1961 to 2017) as well as in Tadong (0.065 ˚C year−1 from 1981 to 2010) stations, while the maximum temperatures showed no trend in Tadong station from 1981 to 2010 which is consistent with the trend in Gangtok station for the overlapped period. However, it was negative for the overall assessed period (− 0.027 ˚C year−1 from 1961 to 2017) in Gangtok. The average temperatures in Gangtok recorded no trend whereas a positive trend (0.035 ˚C year−1 from 1981 to 2010) was observed at Tadong station. A similar positive trend in the average temperatures has been detected at Gangtok also for the overlapped period. Accelerated warming was noticed during the last two decades with an increase in the probability of extreme events of temperatures (minimum, maximum, average) at the higher end. Precipitation was found to be more variable across the observed period and suggested no trend in the study area.
Identifying risk factors for mortality among patients previously hospitalized for a suicide attempt
Authors: Doshi Riddhi P. , Chen Kun , Wang Fei , Schwartz Harold , Herzog Alfred , Aseltine Robert H.
Published: September 2020

Age-adjusted suicide rates in the US have increased over the past two decades across all age groups. The ability to identify risk factors for suicidal behavior is critical to selected and indicated prevention efforts among those at elevated risk of suicide. We used widely available statewide hospitalization data to identify and test the joint predictive power of clinical risk factors associated with death by suicide for patients previously hospitalized for a suicide attempt (N = 19,057). Twenty-eight clinical factors from the prior suicide attempt were found to be significantly associated with the hazard of subsequent suicide mortality. These risk factors and their two-way interactions were used to build a joint predictive model via stepwise regression, in which the predicted individual survival probability was found to be a valid measure of risk for later suicide death. A high-risk group with a four-fold increase in suicide mortality risk was identified based on the out-of-sample predicted survival probabilities. This study demonstrates that the combination of state-level hospital discharge and mortality data can be used to identify suicide attempters who are at high risk of subsequent suicide death.
Predicting the influence of particle size on the glass transition temperature and viscosity of secondary organic material
Authors: Petters Markus , Kasparoglu Sabin
Published: September 2020

Atmospheric aerosols can assume liquid, amorphous semi-solid or glassy, and crystalline phase states. Particle phase state plays a critical role in understanding and predicting aerosol impacts on human health, visibility, cloud formation, and climate. Melting point depression increases with decreasing particle diameter and is predicted by the Gibbs–Thompson relationship. This work reviews existing data on the melting point depression to constrain a simple parameterization of the process. The parameter $$\xi $$
ξ
describes the degree to which particle size lowers the melting point and is found to vary between 300 and 1800 K nm for a wide range of particle compositions. The parameterization is used together with existing frameworks for modeling the temperature and RH dependence of viscosity to predict the influence of particle size on the glass transition temperature and viscosity of secondary organic aerosol formed from the oxidation of $$\alpha $$
α
-pinene. Literature data are broadly consistent with the predictions. The model predicts a sharp decrease in viscosity for particles less than 100 nm in diameter. It is computationally efficient and suitable for inclusion in models to evaluate the potential influence of the phase change on atmospheric processes. New experimental data of the size-dependence of particle viscosity for atmospheric aerosol mimics are needed to thoroughly validate the predictions.
Transcriptomic profile analysis of the halophyte Suaeda rigida response and tolerance under NaCl stress
Authors: Han Zhan-Jiang , Sun Yang , Zhang Min , Zhai Jun-Tuan
Published: September 2020

Suaeda rigida is a lignified, true haplotype that predominantly grows in the Tarim basin, China. It has significant economic and ecological value. Herein, with aim to determine the genes associated with salt tolerance, transcriptome sequencing was performed on its stem, leaves and root over three set NaCl gradients regimens at treatment intervals of 3 h and 5 days. From our findings, we identified 829,095 unigenes, with 331,394 being successfully matched to at least one annotation database. In roots, under 3 h treatment, no up-regulated DEGs were identified in 100 and 500 mM NaCl treated samples. Under 5 days treatment, 97, 60 and 242 up-regulated DEGs were identified in 100, 300, 500 mM NaCl treated samples, respectively. We identified 50, 22 and 255 down-regulated DEGs in 100, 300, 500 mM NaCl treated samples, respectively. GO biological process enrichment analysis established that down-regulated DEGs were associated with nitrogen compound transport, organic substance transport and intracellular protein transport while the up-regulated genes were enriched in cell wall biogenesis, such as plant-type cell wall biogenesis, cell wall assembly, extracellular matrix organization and plant-type cell wall organization. These findings provide valuable knowledge on genes associated with salt tolerance of Suaeda rigida, and can be applied in other downstream haplotype studies.
Integration of voltammetric analysis, protein electrophoresis and pH measurement for diagnosis of pleural effusions: a non-conventional diagnostic approach
Authors: Pipita Maria Elena , Santonico Marco , Pennazza Giorgio , Zompanti Alessandro , Fazzina Sara , Cavalieri Danilo , Bruno Francesca , Angeletti Silvia , Pedone Claudio , Incalzi Raffaele Antonelli
Published: September 2020

Pleural effusion is very common, but an etiologic diagnosis is often difficult. We used three unconventional diagnostic techniques (voltammetric analysis, protein electrophoresis and pH measurement) performed on pleural effusion to do a preliminary distinction between a neoplastic and a non-neoplastic origin. Pleural fluid samples were collected through thoracentesis, thoracoscopy, or post-surgery pleural drainage of 116 patients admitted to acute care wards. Samples were analyzed with the three unconventional techniques: voltammetric analysis using the BIONOTE system, capillary electrophoresis and pH measurement using a potentiometric method. The BIONOTE system is an innovative system that performs a cyclic voltammetric analysis of a biological liquid sample. The final output of the electrochemical analysis is an electrical pattern that represents a fingerprint of the analyzed sample and each sample has a different fingerprint. Data from the three unconventional diagnostic techniques were analyzed using partial least squares discriminant analysis to discriminate neoplastic from non-neoplastic effusions; we also evaluated sensitivity, specificity and percentage of correct classification. The mean age was 68 years (SD: 12); 78 (67.24%) participants were men. Results obtained from all the unconventional techniques employed showed that neoplastic and non-neoplastic pleural effusions were correctly classified in 80.2% of cases, with a sensitivity of 77% and specificity of 83%. The combined use of voltammetric analysis, protein electrophoresis and pH measurement of pleural fluid can easily and quickly distinguish a neoplastic from a non-neoplastic pleural effusion with reliable accuracy and represents an innovative diagnostic approach. In fact, this protocol can be executed in just few minutes directly in the patient's bed and it holds great promise to improve the prognosis and therapeutic chances.
Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum
Authors: Ben Chehida Yacine , Thumloup Julie , Schumacher Cassie , Harkins Timothy , Aguilar Alex , Borrell Asunción , Ferreira Marisa , Rojas-Bracho Lorenzo , Robertson Kelly M. , Taylor Barbara L. , Víkingsson Gísli A. , Weyna Arthur , Romiguier Jonathan , Morin Phillip A. , Fontaine Michael C.
Published: September 2020

Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall’s) and southern species (spectacled and Burmeister’s). In contrast to previous studies, spectacled and Burmeister’s porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall’s, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.
Small-scale volcanic aerosols variability, processes and direct radiative impact at Mount Etna during the EPL-RADIO campaigns
Authors: Sellitto Pasquale , Salerno Giuseppe , La Spina Alessandro , Caltabiano Tommaso , Scollo Simona , Boselli Antonella , Leto Giuseppe , Zanmar Sanchez Ricardo , Crumeyrolle Suzanne , Hanoune Benjamin , Briole Pierre
Published: September 2020

The aerosol properties of Mount Etna’s passive degassing plume and its short-term processes and radiative impact were studied in detail during the EPL-RADIO campaigns (summer 2016–2017), using a synergistic combination of observations and radiative transfer modelling. Summit observations show extremely high particulate matter concentrations. Using portable photometers, the first mapping of small-scale (within $$\sim 20\,\hbox {km}$$

∼
20

km

from the degassing craters) spatial variability of the average size and coarse-to-fine burden proportion of volcanic aerosols is obtained. A substantial variability of the plume properties is found at these spatial scales, revealing that processes (e.g. new particle formation and/or coarse aerosols sedimentation) are at play, which are not represented with current regional scale modelling and satellite observations. Statistically significant progressively smaller particles and decreasing coarse-to-fine particles burden proportion are found along plume dispersion. Vertical structures of typical passive degassing plumes are also obtained using observations from a fixed LiDAR station constrained with quasi-simultaneous photometric observations. These observations are used as input to radiative transfer calculations, to obtain the shortwave top of the atmosphere (TOA) and surface radiative effect of the plume. For a plume with an ultraviolet aerosol optical depth of 0.12–0.14, daily average radiative forcings of $$-\;4.5$$

-

4.5

and $$-\;7.0\,\hbox {W/m}^2$$

-

7.0

W/m
2

, at TOA and surface, are found at a fixed location $$\sim 7\,\hbox {km}$$

∼
7

km

downwind the degassing craters. This is the first available estimation in the literature of the local radiative impact of a passive degassing volcanic plume.
LAMP3 induces apoptosis and autoantigen release in Sjögren’s syndrome patients
Authors: Tanaka Tsutomu , Warner Blake M. , Odani Toshio , Ji Youngmi , Mo Ying-Qian , Nakamura Hiroyuki , Jang Shyh-Ing , Yin Hongen , Michael Drew G. , Hirata Noriyuki , Suizu Futoshi , Ishigaki Satoko , Oliveira Fabiola Reis , Motta Ana Carolina F. , Ribeiro-Silva Alfredo , Rocha Eduardo M. , Atsumi Tatsuya , Noguchi Masayuki , Chiorini John A.
Published: September 2020

Primary Sjögren’s syndrome (pSS) is a complex autoimmune disease characterized by dysfunction of secretory epithelia with only palliative therapy. Patients present with a constellation of symptoms, and the diversity of symptomatic presentation has made it difficult to understand the underlying disease mechanisms. In this study, aggregation of unbiased transcriptome profiling data sets of minor salivary gland biopsies from controls and Sjögren’s syndrome patients identified increased expression of lysosome-associated membrane protein 3 (LAMP3/CD208/DC-LAMP) in a subset of Sjögren’s syndrome cases. Stratification of patients based on their clinical characteristics suggested an association between increased LAMP3 expression and the presence of serum autoantibodies including anti-Ro/SSA, anti-La/SSB, anti-nuclear antibodies. In vitro studies demonstrated that LAMP3 expression induces epithelial cell dysfunction leading to apoptosis. Interestingly, LAMP3 expression resulted in the accumulation and release of intracellular TRIM21 (one component of SSA), La (SSB), and α-fodrin protein, common autoantigens in Sjögren’s syndrome, via extracellular vesicles in an apoptosis-independent mechanism. This study defines a clear role for LAMP3 in the initiation of apoptosis and an independent pathway for the extracellular release of known autoantigens leading to the formation of autoantibodies associated with this disease.

ClinicalTrials.gov Identifier: NCT00001196, NCT00001390, NCT02327884.
IMPROvER: the Integral Membrane Protein Stability Selector
Authors: Harborne Steven P. D. , Strauss Jannik , Boakes Jessica C. , Wright Danielle L. , Henderson James G. , Boivineau Jacques , Jaakola Veli-Pekka , Goldman Adrian
Published: September 2020

Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites. The mix of information IMPROvER uses can be extracted for any helical membrane protein. We have developed the first general-purpose tool for selecting stabilising variants of $$\upalpha$$
α
-helical membrane proteins, increasing efficiency and reducing workload. IMPROvER can be accessed at http://improver.ddns.net/IMPROvER/.
Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)
Authors: Bükücü Şakir Burak , Sütyemez Mehmet , Kefayati Sina , Paizila Aibibula , Jighly Abdulqader , Kafkas Salih
Published: September 2020

Breeding studies in walnut (Juglans regiaL.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits inJuglans regiaL. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.
The effect of Mass Drug Administration for trachoma on antibodies to Chlamydia trachomatis pgp3 in children
Authors: West Sheila K. , Munoz Beatriz , Mkocha Harran , Gaydos Charlotte A. , Quinn Thomas C.
Published: September 2020

A serologic test for antibodies to chlamydia may be a useful tool for trachoma surveillance. However, little is known about the longitudinal stability of antibody status, especially following Mass Drug Administration (MDA), which is critical to understanding serostatus in trachoma-endemic areas. A longitudinal cohort of 1908 children ages 1–9 years in Tanzania from 50 communities were followed at baseline and for 6 months after MDA. They were evaluated for clinical trachoma, conjunctival swabs were tested for chlamydial infection using GeneXpert platform, and blood spots were collected on filter paper and dried to test for antibodies to Chlamydia trachomatis pgp3 using the Luminex platform. 6.3% of children in the study had infection, and coverage with MDA was 97%. 670 (35%) were sero-positive for pgp3 antibodies at baseline, and 4.0% of these seroreverted to negative following MDA. Of those seronegative at baseline, 3.6% seroconverted. The individual change in log median fluorescence intensity(MFI-BG) values was -0.15 overall (p < .001). Seroconversion rates were lower following MDA and seroreversion rates were slightly higher compared to rates in this same cohort in the absence of MDA. MDA has a small effect on reduction of MFI-BG.
Hemoglobin stimulates vigorous growth of Streptococcus pneumoniae and shapes the pathogen's global transcriptome
Authors: Akhter Fahmina , Womack Edroyal , Vidal Jorge E. , Le Breton Yoann , McIver Kevin S. , Pawar Shrikant , Eichenbaum Zehava
Published: September 2020

Streptococcus pneumoniae (Spn) must acquire iron from the host to establish infection. We examined the impact of hemoglobin, the largest iron reservoir in the body, on pneumococcal physiology. Supplementation with hemoglobin allowed Spn to resume growth in an iron-deplete medium. Pneumococcal growth with hemoglobin was unusually robust, exhibiting a prolonged logarithmic growth, higher biomass, and extended viability in both iron-deplete and standard medium. We observed the hemoglobin-dependent response in multiple serotypes, but not with other host proteins, free iron, or heme. Remarkably, hemoglobin induced a sizable transcriptome remodeling, effecting virulence and metabolism in particular genes facilitating host glycoconjugates use. Accordingly, Spn was more adapted to grow on the human α − 1 acid glycoprotein as a sugar source with hemoglobin. A mutant in the hemoglobin/heme-binding protein Spbhp-37 was impaired for growth on heme and hemoglobin iron. The mutant exhibited reduced growth and iron content when grown in THYB and hemoglobin. In summary, the data show that hemoglobin is highly beneficial for Spn cultivation in vitro and suggest that hemoglobin might drive the pathogen adaptation in vivo. The hemoglobin receptor, Spbhp-37, plays a role in mediating the positive influence of hemoglobin. These novel findings provide intriguing insights into pneumococcal interactions with its obligate human host.
Effect of elicitors on holm oak somatic embryo development and efficacy inducing tolerance to Phytophthora cinnamomi
Authors: Morcillo M. , Sales E. , Ponce L. , Guillén A. , Segura J. , Arrillaga I.
Published: September 2020

Holm oak trees (Quercus ilex L.) mortality is increasing worryingly in the Mediterranean area in the last years. To a large degree this mortality is caused by the oomycete Phytophthora spp., which is responsible for forest decline and dieback in evergreen oak forest areas of the southwestern Iberian Peninsula. This study is based on the possibility of applying chemical elicitors or filtered oomycete extracts to holm oak somatic embryos (SE) in order to induce epigenetic memory, priming, that may increase tolerance to the pathogen in future infections. To this end, we first examined the effect of priming treatments on SE development and its oxidative stress state, to avoid elicitors that may cause damage to embryogenic tissues. Both, the sterile oomycete extracts and the chemical elicitor methyl jasmonate (MeJA) did not produce any detrimental effect on SE growth and development, unlike the elicitors benzothiadiazole (BTH) and p-aminobenzoic acid (PABA) that reduced the relative weight gain and resulted in necrotic and deformed SE when were applied at high concentrations (25 µM BTH or 50 µM PABA) in accordance with their high malondialdehyde content. No significant differences among elicitation treatments were found in dual culture bioassays, although those SEs elicited with 50 µM MeJA increased H2O2 production after challenged against active oomycete indicating the activation of stress response. Since this elicitation treatment did not produce any adverse effect in the embryogenic process we suggest that could be used in further priming experiments to produce holm oak plants adapted to biotic stress.
Honey isomaltose contributes to the induction of granulocyte-colony stimulating factor (G-CSF) secretion in the intestinal epithelial cells following honey heating
Authors: Xu Xin , Asai Koshi , Kato Daiki , Ishiuchi Kan’ichiro , Ding Kewen , Tabuchi Yoshiaki , Ota Misato , Makino Toshiaki
Published: September 2020

We have previously discovered that heated honey but not unheated honey could induce the secretion of granulocyte-colony stimulating factor (G-CSF) in the MCE301 intestinal epithelial cells. The objective of this study was to identify compounds in honey that could contribute to this activity. We bought several kinds of commercial honey samples derived from different flowers, as well as corn syrup samples, in the markets of China and Japan, and heated them at 180 °C for 30 min. MCE301 cells were treated with the medium containing the samples, and G-CSF levels in the medium were measured by ELISA. By comparing their activities and sugar contents, we discovered that isomaltose was primarily implicated. The optimum heating conditions for isomaltose were at 180 °C for 60 min or at 200 °C for 15–30 min, and these time- and temperature-dependencies were similar to those of honey in our previous study. When heated isomaltose was partitioned by dialysis, the active ingredients were transferred into a high-molecular-weight fraction. By size-exclusion HPLC analysis, the average molecular weight of heated isomaltose was 790 kDa. When heated isomaltose was hydrolyzed by acids, glucose was subsequently produced. Maltose, sucrose, turanose, and trehalose did not exhibited any activity when heated at 180 °C for 60 min, indicating that the glucose groups with α(1 → 6)-binding in the isomaltose molecule play important roles in its activity when oxidatively polymerized by heat. The stimulating activity of heated isomaltose was inhibited by toll-like receptor 4 (TLR4) inhibitor, suggesting that heated isomaltose activates TLR4 to induce G-CSF. Since G-CSF is clinically used for cancer patients to accelerate their recovery from neutropenia following chemotherapy or accompanied with aplastic anemia, these findings indicate that honey which contains high level of isomaltose could improve immunosuppressive conditions when honey is heated, and that heated isomaltose might be of potential therapeutic use in patients with compromised immunity caused by chemotherapeutic agents.