bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling negative biotic interactions determining soil microbial community assembly and functioning
Authors: Romdhane Sana , Spor Aymé , Aubert Julie , Bru David , Breuil Marie-Christine , Hallin Sara , Mounier Arnaud , Ouadah Sarah , Tsiknia Myrto , Philippot Laurent 
Published: July 2021

Abstract
Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.
miR-526b-3p inhibits lung cancer cisplatin-resistance and metastasis by inhibiting STAT3-promoted PD-L1
Authors: Chen Kuan-bing , Yang Wei , Xuan Ying , Lin Ai-jun 
Published: July 2021

AbstractChemotherapy remains the primary treatment of advanced solid cancer, including lung cancer. However, as first-line treatment, cisplatin-based therapy is restricted by the frequent development of drug resistance. Increasing data showed that the programmed cell death protein ligand 1 (PD-L1) plays a vital role in regulating cisplatin resistance. However, the underlying mechanisms are not fully understood. We found that miR-526b-3p expression declined while PD-L1 was elevated in cisplatin-resistant lung cancer compared to that in cisplatin-sensitive lung cancer by analyzing clinical samples. Significantly, miR-526b-3p was associated with response to cisplatin negatively. We further demonstrated that miR-526b-3p reversed cisplatin resistance, suppressed metastasis, and activated CD8+ T cells in a STAT3/PD-L1-dependent manner. Thus, our findings extended the knowledge of PD-L1-mediated cisplatin resistance of lung cancer. In addition, the introduction of miR-526b-3p provided a new clue to improve the anti-tumor effects of the combination of immunotherapy and chemotherapy.
Anthropogenic forcing and response yield observed positive trend in Earth’s energy imbalance
Authors: Raghuraman Shiv Priyam , Paynter David , Ramaswamy V. 
Published: July 2021

AbstractThe observed trend in Earth’s energy imbalance (TEEI), a measure of the acceleration of heat uptake by the planet, is a fundamental indicator of perturbations to climate. Satellite observations (2001–2020) reveal a significant positive globally-averaged TEEI of 0.38 ± 0.24 Wm−2decade−1, but the contributing drivers have yet to be understood. Using climate model simulations, we show that it is exceptionally unlikely (<1% probability) that this trend can be explained by internal variability. Instead, TEEI is achieved only upon accounting for the increase in anthropogenic radiative forcing and the associated climate response. TEEI is driven by a large decrease in reflected solar radiation and a small increase in emitted infrared radiation. This is because recent changes in forcing and feedbacks are additive in the solar spectrum, while being nearly offset by each other in the infrared. We conclude that the satellite record provides clear evidence of a human-influenced climate system.
Large linear non-saturating magnetoresistance and high mobility in ferromagnetic MnBi
Authors: He Yangkun , Gayles Jacob , Yao Mengyu , Helm Toni , Reimann Tommy , Strocov Vladimir N. , Schnelle Walter , Nicklas Michael , Sun Yan , Fecher Gerhard H. , Felser Claudia 
Published: July 2021

AbstractA large non-saturating magnetoresistance has been observed in several nonmagnetic topological Weyl semi-metals with high mobility of charge carriers at the Fermi energy. However, ferromagnetic systems rarely display a large magnetoresistance because of localized electrons in heavy d bands with a low Fermi velocity. Here, we report a large linear non-saturating magnetoresistance and high mobility in ferromagnetic MnBi. MnBi, unlike conventional ferromagnets, exhibits a large linear non-saturating magnetoresistance of 5000% under a pulsed field of 70 T. The electrons and holes’ mobilities are both 5000 cm2V−1s−1 at 2 K, which are one of the highest for ferromagnetic materials. These phenomena are due to the spin-polarised Bi 6p band’s sharp dispersion with a small effective mass. Our study provides an approach to achieve high mobility in ferromagnetic systems with a high Curie temperature, which is advantageous for topological spintronics.
SUMOylation of SAMHD1 at Lysine 595 is required for HIV-1 restriction in non-cycling cells
Authors: Martinat Charlotte , Cormier Arthur , Tobaly-Tapiero Joëlle , Palmic Noé , Casartelli Nicoletta , Mahboubi Bijan , Coggins Si’Ana A. , Buchrieser Julian , Persaud Mirjana , Diaz-Griffero Felipe , Espert Lucile , Bossis Guillaume , Lesage Pascale , Schwartz Olivier , Kim Baek , Margottin-Goguet Florence , Saïb Ali , Zamborlini Alessia 
Published: July 2021

AbstractSAMHD1 is a cellular triphosphohydrolase (dNTPase) proposed to inhibit HIV-1 reverse transcription in non-cycling immune cells by limiting the supply of the dNTP substrates. Yet, phosphorylation of T592 downregulates SAMHD1 antiviral activity, but not its dNTPase function, implying that additional mechanisms contribute to viral restriction. Here, we show that SAMHD1 is SUMOylated on residue K595, a modification that relies on the presence of a proximal SUMO-interacting motif (SIM). Loss of K595 SUMOylation suppresses the restriction activity of SAMHD1, even in the context of the constitutively active phospho-ablative T592A mutant but has no impact on dNTP depletion. Conversely, the artificial fusion of SUMO2 to a non-SUMOylatable inactive SAMHD1 variant restores its antiviral function, a phenotype that is reversed by the phosphomimetic T592E mutation. Collectively, our observations clearly establish that lack of T592 phosphorylation cannot fully account for the restriction activity of SAMHD1. We find that SUMOylation of K595 is required to stimulate a dNTPase-independent antiviral activity in non-cycling immune cells, an effect that is antagonized by cyclin/CDK-dependent phosphorylation of T592 in cycling cells.
Stearic acid blunts growth-factor signaling via oleoylation of GNAI proteins
Authors: Nůsková Hana , Serebryakova Marina V. , Ferrer-Caelles Anna , Sachsenheimer Timo , Lüchtenborg Christian , Miller Aubry K. , Brügger Britta , Kordyukova Larisa V. , Teleman Aurelio A. 
Published: July 2021

AbstractCovalent attachment of C16:0 to proteins (palmitoylation) regulates protein function. Proteins are also S-acylated by other fatty acids including C18:0. Whether protein acylation with different fatty acids has different functional outcomes is not well studied. We show here that C18:0 (stearate) and C18:1 (oleate) compete with C16:0 to S-acylate Cys3 of GNAI proteins. C18:0 becomes desaturated so that C18:0 and C18:1 both cause S-oleoylation of GNAI. Exposure of cells to C16:0 or C18:0 shifts GNAI acylation towards palmitoylation or oleoylation, respectively. Oleoylation causes GNAI proteins to shift out of cell membrane detergent-resistant fractions where they potentiate EGFR signaling. Consequently, exposure of cells to C18:0 reduces recruitment of Gab1 to EGFR and reduces AKT activation. This provides a molecular mechanism for the anti-tumor effects of C18:0, uncovers a mechanistic link how metabolites affect cell signaling, and provides evidence that the identity of the fatty acid acylating a protein can have functional consequences.
An umbrella review of the evidence associating diet and cancer risk at 11 anatomical sites
Authors: Papadimitriou Nikos , Markozannes Georgios , Kanellopoulou Afroditi , Critselis Elena , Alhardan Sumayah , Karafousia Vaia , Kasimis John C. , Katsaraki Chrysavgi , Papadopoulou Areti , Zografou Maria , Lopez David S. , Chan Doris S. M. , Kyrgiou Maria , Ntzani Evangelia , Cross Amanda J. , Marrone Michael T. , Platz Elizabeth A. , Gunter Marc J. , Tsilidis Konstantinos K. 
Published: July 2021

AbstractThere is evidence that diet and nutrition are modifiable risk factors for several cancers, but associations may be flawed due to inherent biases. Nutritional epidemiology studies have largely relied on a single assessment of diet using food frequency questionnaires. We conduct an umbrella review of meta-analyses of observational studies to evaluate the strength and validity of the evidence for the association between food/nutrient intake and risk of developing or dying from 11 primary cancers. It is estimated that only few single food/nutrient and cancer associations are supported by strong or highly suggestive meta-analytic evidence, and future similar research is unlikely to change this evidence. Alcohol consumption is positively associated with risk of postmenopausal breast, colorectal, esophageal, head & neck and liver cancer. Consumption of dairy products, milk, calcium and wholegrains are inversely associated with colorectal cancer risk. Coffee consumption is inversely associated with risk of liver cancer and skin basal cell carcinoma.
Cardiac-specific deletion of voltage dependent anion channel 2 leads to dilated cardiomyopathy by altering calcium homeostasis
Authors: Shankar Thirupura S. , Ramadurai Dinesh K. A. , Steinhorst Kira , Sommakia Salah , Badolia Rachit , Thodou Krokidi Aspasia , Calder Dallen , Navankasattusas Sutip , Sander Paulina , Kwon Oh Sung , Aravamudhan Aishwarya , Ling Jing , Dendorfer Andreas , Xie Changmin , Kwon Ohyun , Cheng Emily H. Y. , Whitehead Kevin J. , Gudermann Thomas , Richardson Russel S. , Sachse Frank B. , Schredelseker Johann , Spitzer Kenneth W. , Chaudhuri Dipayan , Drakos Stavros G. 
Published: July 2021

AbstractVoltage dependent anion channel 2 (VDAC2) is an outer mitochondrial membrane porin known to play a significant role in apoptosis and calcium signaling. Abnormalities in calcium homeostasis often leads to electrical and contractile dysfunction and can cause dilated cardiomyopathy and heart failure. However, the specific role of VDAC2 in intracellular calcium dynamics and cardiac function is not well understood. To elucidate the role of VDAC2 in calcium homeostasis, we generated a cardiac ventricular myocyte-specific developmental deletion of Vdac2 in mice. Our results indicate that loss of VDAC2 in the myocardium causes severe impairment in excitation-contraction coupling by altering both intracellular and mitochondrial calcium signaling. We also observed adverse cardiac remodeling which progressed to severe cardiomyopathy and death. Reintroduction of VDAC2 in 6-week-old knock-out mice partially rescued the cardiomyopathy phenotype. Activation of VDAC2 by efsevin increased cardiac contractile force in a mouse model of pressure-overload induced heart failure. In conclusion, our findings demonstrate that VDAC2 plays a crucial role in cardiac function by influencing cellular calcium signaling. Through this unique role in cellular calcium dynamics and excitation-contraction coupling VDAC2 emerges as a plausible therapeutic target for heart failure.
Neural and computational mechanisms of momentary fatigue and persistence in effort-based choice
Authors: Müller Tanja , Klein-Flügge Miriam C. , Manohar Sanjay G. , Husain Masud , Apps Matthew A. J. 
Published: July 2021

AbstractFrom a gym workout, to deciding whether to persevere at work, many activities require us to persist in deciding that rewards are ‘worth the effort’ even as we become fatigued. However, studies examining effort-based decisions typically assume that the willingness to work is static. Here, we use computational modelling on two effort-based tasks, one behavioural and one during fMRI. We show that two hidden states of fatigue fluctuate on a moment-to-moment basis on different timescales but both reduce the willingness to exert effort for reward. The value of one state increases after effort but is ‘recoverable’ by rests, whereas a second ‘unrecoverable’ state gradually increases with work. The BOLD response in separate medial and lateral frontal sub-regions covaried with these states when making effort-based decisions, while a distinct fronto-striatal system integrated fatigue with value. These results provide a computational framework for understanding the brain mechanisms of persistence and momentary fatigue.
Study on environmental behaviour of fluopyram in different banana planting soil
Authors: Zhou Jia , Liang Shuilian , Cui Yuanyuan , Rong Yu , Song Jia , Lv Daizhu 
Published: July 2021

AbstractFluopyram is commonly used to control banana leaf spot, anthracnose, and scab in tropical agricultural areas. To explore its behaviour in tropical agricultural environments, dissipation, adsorption, and leaching behaviours of fluopyram in three typical banana planting soils were studied. Also, its dissipation and migration capabilities in different regions and different soil types were evaluated. The results showed that the dissipation of fluopyram was in accordance with the first-order kinetic equation in the three banana soils, but the degradation rates were quite different. The degradation half-lives in the Hainan latosol, Yunnan sandy soil, and Fujian Plain alluvial soil were 46.21 days, 36.48 days and 57.76 days, respectively. Fluopyram also exhibited high adsorption and low leachability in the three soils. The Fujian Plain alluvial soil had the highest adsorption capacity for fluopyram, while fluopyram had the low leachability in the Yunnan sandy soil.
Elevated levels of Merkel cell polyoma virus in the anophthalmic conjunctiva
Authors: Siegal Nora , Gutowski Michal , Akileswaran Lakshmi , Beauchamp Norman J. , Ding Lien-Chieh , Chambers Christopher B. , Van Gelder Russell N. 
Published: July 2021

AbstractThe human ocular surface hosts a paucibacterial resident microbiome and virome. The factors contributing to homeostasis of this mucosal community are presently unknown. To determine the impact of ocular enucleation and prosthesis placement on the ocular surface microbiome, we sampled conjunctival swabs from 20 anophthalmic and 20 fellow-eye intact conjunctiva. DNA was extracted and subjected to quantitative 16S rDNA PCR, biome representational karyotyping (BRiSK), and quantitative PCR (qPCR) confirmation of specific organisms. 16S ribosomal qPCR revealed equivalent bacterial loads between conditions. Biome representational in silico karyotyping (BRiSK) demonstrated comparable bacterial fauna between anophthalmic and intact conjunctiva. Both torque teno virus and Merkel cell polyoma virus (MCPyV) were detected frequently in healthy and anophthalmic conjunctiva. By qPCR, MCPyV was detected in 19/20 anophthalmic samples compared with 5/20 fellow eyes. MCPyV copy number averaged 891 copies/ng in anophthalmic conjunctiva compared with 193 copies/ng in fellow eyes (p < 0.001). These results suggest that enucleation and prosthesis placement affect the ocular surface flora, particularly for the resident virome. As MCPyV has been shown to be the etiologic cause of Merkel cell carcinoma, understanding the mechanisms by which the ocular surface regulates this virus may have clinical importance.
Combining a convolutional neural network with autoencoders to predict the survival chance of COVID-19 patients
Authors: Khozeimeh Fahime , Sharifrazi Danial , Izadi Navid Hoseini , Joloudari Javad Hassannataj , Shoeibi Afshin , Alizadehsani Roohallah , Gorriz Juan M. , Hussain Sadiq , Sani Zahra Alizadeh , Moosaei Hossein , Khosravi Abbas , Nahavandi Saeid , Islam Sheikh Mohammed Shariful 
Published: July 2021

AbstractCOVID-19 has caused many deaths worldwide. The automation of the diagnosis of this virus is highly desired. Convolutional neural networks (CNNs) have shown outstanding classification performance on image datasets. To date, it appears that COVID computer-aided diagnosis systems based on CNNs and clinical information have not yet been analysed or explored. We propose a novel method, named the CNN-AE, to predict the survival chance of COVID-19 patients using a CNN trained with clinical information. Notably, the required resources to prepare CT images are expensive and limited compared to those required to collect clinical data, such as blood pressure, liver disease, etc. We evaluated our method using a publicly available clinical dataset that we collected. The dataset properties were carefully analysed to extract important features and compute the correlations of features. A data augmentation procedure based on autoencoders (AEs) was proposed to balance the dataset. The experimental results revealed that the average accuracy of the CNN-AE (96.05%) was higher than that of the CNN (92.49%). To demonstrate the generality of our augmentation method, we trained some existing mortality risk prediction methods on our dataset (with and without data augmentation) and compared their performances. We also evaluated our method using another dataset for further generality verification. To show that clinical data can be used for COVID-19 survival chance prediction, the CNN-AE was compared with multiple pre-trained deep models that were tuned based on CT images.
Association between comorbid asthma and prognosis of critically ill patients with severe sepsis: a cohort study
Authors: Huang Jinju , Zhang Jurong , Wang Faxia , Liang Jiezhu , Chen Qinchang , Lin Zhuandi 
Published: July 2021

AbstractBasic research suggests some contributing mechanisms underlying asthma might at the same time benefit patients with asthma against sepsis, while the potential protective effect of comorbid asthma on prognosis of sepsis has not been well studied in clinical research. The study aimed to assess the association between comorbid asthma and prognosis in a cohort of patients admitted to intensive care unit (ICU) with severe sepsis. Patients with severe sepsis admitted to ICUs were included from the MIMIC-III Critical Care Database, and categorized as patients without asthma, patients with stable asthma, and patients with acute exacerbation asthma. The primary study outcome was 28-day mortality since ICU admission. Difference in survival distributions among groups were evaluated by Kaplan–Meier estimator. Multivariable Cox regression was employed to examine the association between comorbid asthma and prognosis. A total of 2469 patients with severe sepsis were included, of which 2327 (94.25%) were without asthma, 125 (5.06%) with stable asthma, and 17 (0.69%) with acute exacerbation asthma. Compared with patients without asthma, patients with asthma (either stable or not) had a slightly younger age (66.73 ± 16.32 versus 64.77 ± 14.81 years), a lower proportion of male sex (56.81% versus 40.14%), and a lower median SAPS II score (46 versus 43). Patients with acute exacerbation asthma saw the highest 28-day mortality rate (35.29%), but patients with stable asthma had the lowest 28-day mortality rate (21.60%) when compared to that (34.42%) in patients without asthma. Consistent results were observed in Kaplan–Meier curves with a p-value for log-rank test of 0.016. After adjusting for potential confounding, compared to being without asthma, being with stable asthma was associated with a reduced risk of 28-day mortality (hazard ratio (HR) 0.65, 95% confidence interval (CI) 0.44–0.97, p = 0.0335), but being with acute exacerbation asthma was toward an increased risk of 28-day mortality (HR 1.82, 95% 0.80–4.10, p = 0.1513). E-value analysis suggested robustness to unmeasured confounding. These findings suggest comorbid stable asthma is associated with a better prognosis in critically ill patients with severe sepsis, while acute exacerbation asthma is associated with worse prognosis.
A dielectric free near field phase transforming structure for wideband gain enhancement of antennas
Authors: Ahmed Foez , Afzal Muhammad U. , Hayat Touseef , Esselle Karu P. , Thalakotuna Dushmantha N. 
Published: July 2021

AbstractThe gain of some aperture antennas can be significantly increased by making the antenna near-field phase distribution more uniform, using a phase-transformation structure. A novel dielectric-free phase transforming structure (DF-PTS) is presented in this paper for this purpose, and its ability to correct the aperture phase distribution of a resonant cavity antenna (RCA) over a much wider bandwidth is demonstrated. As opposed to printed multilayered metasurfaces, all the cells in crucial locations of the DF-PTS have a phase response that tracks the phase error of the RCA over a large bandwidth, and in addition have wideband transmission characteristics, resulting in a wideband antenna system. The new DF-PTS, made of three thin metal sheets each containing modified-eight-arm-asterisk-shaped slots, is significantly stronger than the previous DF-PTS, which requires thin and long metal interconnects between metal patches. The third advantage of the new DF-PTS is, all phase transformation cells in it are highly transparent, each with a transmission magnitude greater than − 1 dB at the design frequency, ensuring excellent phase correction with minimal effect on aperture amplitude distribution. With the DF-PTS, RCA gain increases to 20.1 dBi, which is significantly greater than its 10.7 dBi gain without the DF-PTS. The measured 10-dB return loss bandwidth and the 3-dB gain bandwidth of the RCA with DF-PTS are 46% and 12%, respectively.
The first draft genome of feather grasses using SMRT sequencing and its implications in molecular studies of Stipa
Authors: Baiakhmetov Evgenii , Guyomar Cervin , Shelest Ekaterina , Nobis Marcin , Gudkova Polina D. 
Published: July 2021

AbstractThe Eurasian plant Stipa capillata is the most widespread species within feather grasses. Many taxa of the genus are dominants in steppe plant communities and can be used for their classification and in studies related to climate change. Moreover, some species are of economic importance mainly as fodder plants and can be used for soil remediation processes. Although large-scale molecular data has begun to appear, there is still no complete or draft genome for any Stipa species. Thus, here we present a single-molecule long-read sequencing dataset generated using the Pacific Biosciences Sequel System. A draft genome of about 1004 Mb was obtained with a contig N50 length of 351 kb. Importantly, here we report 81,224 annotated protein-coding genes, present 77,614 perfect and 58 unique imperfect SSRs, reveal the putative allopolyploid nature of S. capillata, investigate the evolutionary history of the genus, demonstrate structural heteroplasmy of the chloroplast genome and announce for the first time the mitochondrial genome in Stipa. The assembled nuclear, mitochondrial and chloroplast genomes provide a significant source of genetic data for further works on phylogeny, hybridisation and population studies within Stipa and the grass family Poaceae.