bluuebunny/crossref_metadata_2025 huggingface dataset:
Bone marrow mesenchymal stem cells-derived exosomal microRNA-193a reduces cisplatin resistance of non-small cell lung cancer cells via targeting LRRC1
Authors: Wu Hongbo , Mu Xiaoqian , Liu Lei , Wu Huijuan , Hu Xiufeng , Chen Lijuan , Liu Jie , Mu Yu , Yuan Fangfang , Liu Wenjing , Zhao Yanqiu
Published: September 2020

Exosomes are small endogenous membrane vesicles that can mediate cell communication by transferring genetic materials. Based on that, exosomes have always been discussed as a cargo carrier for microRNA (miRNA) transportation. Accumulating data have reported the inhibitory effects of microRNA-193a (miR-193a) on non-small cell lung cancer (NSCLC) cell progression. However, the mechanisms of miR-193a delivery to cancer cells and miR-193a in exosomes have not been explored clearly in NSCLC. Given that, this work aims to decode exosomal miR-193a in cisplatin (DDP) resistance of NSCLC cells. A549 and H1299 cell lines were screened out and their parent cells and drug-resistant cells were co-cultured with human bone marrow mesenchymal stem cells (BMSCs)-derived exosomes (BMSC-Exo) that had been transfected with miR-193a mimic or si-LRRC1 to detect the colony formation, migration, apoptosis, invasion and proliferation of NSCLC cells. In vivo experiment was conducted to verify the in vitro results. BMSC-Exo with upregulated miR-193a and downregulated LRRC1 suppressed colony formation, invasion, proliferation and migration as well as advanced apoptosis of NSCLC parent cells and drug-resistant cells. BMSC-Exo combined with upregulated miR-193a reduced tumor volume and weight in mice with NSCLC. Functional studies report that BMSC-Exo shuffle miR-193a to suppress the colony formation, invasion, migration, and proliferation as well as advance apoptosis of NSCLC DDP-resistant cells via downregulating LRRC1.
Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism
Authors: Zhang Jie , Petersen Søren D. , Radivojevic Tijana , Ramirez Andrés , Pérez-Manríquez Andrés , Abeliuk Eduardo , Sánchez Benjamín J. , Costello Zak , Chen Yu , Fero Michael J. , Martin Hector Garcia , Nielsen Jens , Keasling Jay D. , Jensen Michael K.
Published: September 2020

Through advanced mechanistic modeling and the generation of large high-quality datasets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show that mechanistic and machine learning models can be combined to enable accurate genotype-to-phenotype predictions. We use a genome-scale model to pinpoint engineering targets, efficient library construction of metabolic pathway designs, and high-throughput biosensor-enabled screening for training diverse machine learning algorithms. From a single data-generation cycle, this enables successful forward engineering of complex aromatic amino acid metabolism in yeast, with the best machine learning-guided design recommendations improving tryptophan titer and productivity by up to 74 and 43%, respectively, compared to the best designs used for algorithm training. Thus, this study highlights the power of combining mechanistic and machine learning models to effectively direct metabolic engineering efforts.
A machine learning Automated Recommendation Tool for synthetic biology
Authors: Radivojević Tijana , Costello Zak , Workman Kenneth , Garcia Martin Hector
Published: September 2020

Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc engineering practices, which lead to long development times. Here, we present the Automated Recommendation Tool (ART), a tool that leverages machine learning and probabilistic modeling techniques to guide synthetic biology in a systematic fashion, without the need for a full mechanistic understanding of the biological system. Using sampling-based optimization, ART provides a set of recommended strains to be built in the next engineering cycle, alongside probabilistic predictions of their production levels. We demonstrate the capabilities of ART on simulated data sets, as well as experimental data from real metabolic engineering projects producing renewable biofuels, hoppy flavored beer without hops, fatty acids, and tryptophan. Finally, we discuss the limitations of this approach, and the practical consequences of the underlying assumptions failing.
A data-driven simulation platform to predict cultivars’ performances under uncertain weather conditions
Authors: de los Campos Gustavo , Pérez-Rodríguez Paulino , Bogard Matthieu , Gouache David , Crossa José
Published: September 2020

In most crops, genetic and environmental factors interact in complex ways giving rise to substantial genotype-by-environment interactions (G×E). We propose that computer simulations leveraging field trial data, DNA sequences, and historical weather records can be used to tackle the longstanding problem of predicting cultivars’ future performances under largely uncertain weather conditions. We present a computer simulation platform that uses Monte Carlo methods to integrate uncertainty about future weather conditions and model parameters. We use extensive experimental wheat yield data (n = 25,841) to learn G×E patterns and validate, using left-trial-out cross-validation, the predictive performance of the model. Subsequently, we use the fitted model to generate circa 143 million grain yield data points for 28 wheat genotypes in 16 locations in France, over 16 years of historical weather records. The phenotypes generated by the simulation platform have multiple downstream uses; we illustrate this by predicting the distribution of expected yield at 448 cultivar-location combinations and performing means-stability analyses.
Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism
Authors: Ramaswami Gokul , Won Hyejung , Gandal Michael J. , Haney Jillian , Wang Jerry C. , Wong Chloe C. Y. , Sun Wenjie , Prabhakar Shyam , Mill Jonathan , Geschwind Daniel H.
Published: September 2020

Autism spectrum disorder (ASD) is a phenotypically and genetically heterogeneous neurodevelopmental disorder. Despite this heterogeneity, previous studies have shown patterns of molecular convergence in post-mortem brain tissue from autistic subjects. Here, we integrate genome-wide measures of mRNA expression, miRNA expression, DNA methylation, and histone acetylation from ASD and control brains to identify a convergent molecular subtype of ASD with shared dysregulation across both the epigenome and transcriptome. Focusing on this convergent subtype, we substantially expand the repertoire of differentially expressed genes in ASD and identify a component of upregulated immune processes that are associated with hypomethylation. We utilize eQTL and chromosome conformation datasets to link differentially acetylated regions with their cognate genes and identify an enrichment of ASD genetic risk variants in hyperacetylated noncoding regulatory regions linked to neuronal genes. These findings help elucidate how diverse genetic risk factors converge onto specific molecular processes in ASD.
Transition from light diffusion to localization in three-dimensional amorphous dielectric networks near the band edge
Authors: Haberko Jakub , Froufe-Pérez Luis S. , Scheffold Frank
Published: September 2020

Localization of light is the photon analog of electron localization in disordered lattices, for whose discovery Anderson received the Nobel prize in 1977. The question about its existence in open three-dimensional materials has eluded an experimental and full theoretical verification for decades. Here we study numerically electromagnetic vector wave transmittance through realistic digital representations of hyperuniform dielectric networks, a new class of highly correlated but disordered photonic band gap materials. We identify the evanescent decay of the transmitted power in the gap and diffusive transport far from the gap. Near the gap, we find that transport sets off diffusive but, with increasing slab thickness, crosses over gradually to a faster decay, signaling localization. We show that we can describe the transition to localization at the mobility edge using the self-consistent theory of localization based on the concept of a position-dependent diffusion coefficient.
Trait phenomenological control predicts experience of mirror synaesthesia and the rubber hand illusion
Authors: Lush P. , Botan V. , Scott R. B. , Seth A. K. , Ward J. , Dienes Z.
Published: September 2020

In hypnotic responding, expectancies arising from imaginative suggestion drive striking experiential changes (e.g., hallucinations) — which are experienced as involuntary — according to a normally distributed and stable trait ability (hypnotisability). Such experiences can be triggered by implicit suggestion and occur outside the hypnotic context. In large sample studies (of 156, 404 and 353 participants), we report substantial relationships between hypnotisability and experimental measures of experiential change in mirror-sensory synaesthesia and the rubber hand illusion comparable to relationships between hypnotisability and individual hypnosis scale items. The control of phenomenology to meet expectancies arising from perceived task requirements can account for experiential change in psychological experiments.
The atypical chemokine receptor 3 interacts with Connexin 43 inhibiting astrocytic gap junctional intercellular communication
Authors: Fumagalli Amos , Heuninck Joyce , Pizzoccaro Anne , Moutin Enora , Koenen Joyce , Séveno Martial , Durroux Thierry , Junier Marie-Pierre , Schlecht-Louf Géraldine , Bachelerie Francoise , Schütz Dagmar , Stumm Ralf , Smit Martine J. , Guérineau Nathalie C. , Chaumont-Dubel Séverine , Marin Philippe
Published: September 2020

The atypical chemokine receptor 3 (ACKR3) plays a pivotal role in directing the migration of various cellular populations and its over-expression in tumors promotes cell proliferation and invasiveness. The intracellular signaling pathways transducing ACKR3-dependent effects remain poorly characterized, an issue we addressed by identifying the interactome of ACKR3. Here, we report that recombinant ACKR3 expressed in HEK293T cells recruits the gap junction protein Connexin 43 (Cx43). Cx43 and ACKR3 are co-expressed in mouse brain astrocytes and human glioblastoma cells and form a complex in embryonic mouse brain. Functional in vitro studies show enhanced ACKR3 interaction with Cx43 upon ACKR3 agonist stimulation. Furthermore, ACKR3 activation promotes β-arrestin2- and dynamin-dependent Cx43 internalization to inhibit gap junctional intercellular communication in primary astrocytes. These results demonstrate a functional link between ACKR3 and gap junctions that might be of pathophysiological relevance.
Characterization of BRCA1-deficient premalignant tissues and cancers identifies Plekha5 as a tumor metastasis suppressor
Authors: Liu Jianlin , Adhav Ragini , Miao Kai , Su Sek Man , Mo Lihua , Chan Un In , Zhang Xin , Xu Jun , Li Jianjie , Shu Xiaodong , Zeng Jianming , Zhang Xu , Lyu Xueying , Pardeshi Lakhansing , Tan Kaeling , Sun Heng , Wong Koon Ho , Deng Chuxia , Xu Xiaoling
Published: September 2020

Single-cell whole-exome sequencing (scWES) is a powerful approach for deciphering intratumor heterogeneity and identifying cancer drivers. So far, however, simultaneous analysis of single nucleotide variants (SNVs) and copy number variations (CNVs) of a single cell has been challenging. By analyzing SNVs and CNVs simultaneously in bulk and single cells of premalignant tissues and tumors from mouse and human BRCA1-associated breast cancers, we discover an evolution process through which the tumors initiate from cells with SNVs affecting driver genes in the premalignant stage and malignantly progress later via CNVs acquired in chromosome regions with cancer driver genes. These events occur randomly and hit many putative cancer drivers besides p53 to generate unique genetic and pathological features for each tumor. Upon this, we finally identify a tumor metastasis suppressor Plekha5, whose deficiency promotes cancer metastasis to the liver and/or lung.
Face selective patches in marmoset frontal cortex
Authors: Schaeffer David J. , Selvanayagam Janahan , Johnston Kevin D. , Menon Ravi S. , Freiwald Winrich A. , Everling Stefan
Published: September 2020

In humans and macaque monkeys, socially relevant face processing is accomplished via a distributed functional network that includes specialized patches in frontal cortex. It is unclear whether a similar network exists in New World primates, who diverged ~35 million years from Old World primates. The common marmoset is a New World primate species ideally placed to address this question given their complex social repertoire. Here, we demonstrate the existence of a putative high-level face processing network in marmosets. Like Old World primates, marmosets show differential activation in anterior cingulate and lateral prefrontal cortices while they view socially relevant videos of marmoset faces. We corroborate the locations of these frontal regions by demonstrating functional and structural connectivity between these regions and temporal lobe face patches. Given the evolutionary separation between macaques and marmosets, our results suggest this frontal network specialized for social face processing predates the separation between Platyrrhini and Catarrhini.
Yeast homologs of human MCUR1 regulate mitochondrial proline metabolism
Authors: Zulkifli Mohammad , Neff John K. , Timbalia Shrishiv A. , Garza Natalie M. , Chen Yingqi , Watrous Jeramie D. , Murgia Marta , Trivedi Prachi P. , Anderson Steven K. , Tomar Dhanendra , Nilsson Roland , Madesh Muniswamy , Jain Mohit , Gohil Vishal M.
Published: September 2020

Mitochondria house evolutionarily conserved pathways of carbon and nitrogen metabolism that drive cellular energy production. Mitochondrial bioenergetics is regulated by calcium uptake through the mitochondrial calcium uniporter (MCU), a multi-protein complex whose assembly in the inner mitochondrial membrane is facilitated by the scaffold factor MCUR1. Intriguingly, many fungi that lack MCU contain MCUR1 homologs, suggesting alternate functions. Herein, we characterize Saccharomyces cerevisiae homologs Put6 and Put7 of MCUR1 as regulators of mitochondrial proline metabolism. Put6 and Put7 are tethered to the inner mitochondrial membrane in a large hetero-oligomeric complex, whose abundance is regulated by proline. Loss of this complex perturbs mitochondrial proline homeostasis and cellular redox balance. Yeast cells lacking either Put6 or Put7 exhibit a pronounced defect in proline utilization, which can be corrected by the heterologous expression of human MCUR1. Our work uncovers an unexpected role of MCUR1 homologs in mitochondrial proline metabolism.
Author Correction: A possible association between fructose consumption and pulmonary emphysema
Authors: Suehiro Camila Liyoko , de Toledo-Arruda Alessandra Choqueta , Vieira Rodolfo de Paula , de Almeida Francine Maria , Olivo Clarice Rosa , de Arruda Martins Milton , Lin Chin Jia
Published: September 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Comparative analysis of rhizosphere soil physiochemical characteristics and microbial communities between rusty and healthy ginseng root
Authors: Bian Xingbo , Xiao Shengyuan , Zhao Yan , Xu Yonghua , Yang He , Zhang Lianxue
Published: September 2020

Ginseng rusty root (GRR) symptom is one of the primary diseases of ginseng. There has been a problem of ginseng rusty root, leading to a severe decline in the quality of ginseng. To clarify the relationship between root symptoms of ginseng rust and soil, the physical and chemical properties, enzyme activity, community structure and microbial diversity of GRR and healthy ginseng (HG) rhizosphere soil were analyzed and compared. The pH and redox potential (Eh) of GRR soil decreased, and the contents of total phosphorus (TP), available phosphorus (AP), and available potassium (AK) decreased. The activity of catalase and phosphatase and invertase was lower than that of HG groups. Besides, the microbial community of GRR rhizosphere soil changes much, and its abundance and diversity are significantly reduced. The community structure of GRR rhizosphere soil also shows apparent differences, and the samples of the HG group gathered together, and the samples of the GRR group were dispersed. In general, GRR was closely associated with decreases in soil pH and Eh; decreases in TP, AP, and AK; decreases in the activity of several enzymes. Additionally, it is strongly associated with an increase in pathogenic microorganisms such as Ilyonectria and a reduction of beneficial microorganisms such as Tremellomycetes Acidobacteria subgroup 6 and Gemmatimonadetes.
Efficiency of the four proteasome subtypes to degrade ubiquitinated or oxidized proteins
Authors: Abi Habib Joanna , De Plaen Etienne , Stroobant Vincent , Zivkovic Dusan , Bousquet Marie-Pierre , Guillaume Benoît , Wahni Khadija , Messens Joris , Busse Antonia , Vigneron Nathalie , Van den Eynde Benoit J.
Published: September 2020

The proteasome is responsible for selective degradation of proteins. It exists in mammalian cells under four main subtypes, which differ by the combination of their catalytic subunits: the standard proteasome (β1–β2–β5), the immunoproteasome (β1i–β2i–β5i) and the two intermediate proteasomes (β1–β2–β5i and β1i–β2–β5i). The efficiency of the four proteasome subtypes to degrade ubiquitinated or oxidized proteins remains unclear. Using cells expressing exclusively one proteasome subtype, we observed that ubiquitinated p21 and c-­myc were degraded at similar rates, indicating that the four 26S proteasomes degrade ubiquitinated proteins equally well. Under oxidative stress, we observed a partial dissociation of 26S into 20S proteasomes, which can degrade non-ubiquitinated oxidized proteins. Oxidized calmodulin and hemoglobin were best degraded in vitro by the three β5i-containing 20S proteasomes, while their native forms were not degraded. Circular dichroism analyses indicated that ubiquitin-independent recognition of oxidized proteins by 20S proteasomes was triggered by the disruption of their structure. Accordingly, β5i-containing 20S proteasomes degraded unoxidized naturally disordered protein tau, while 26S proteasomes did not. Our results suggest that the three β5i-containing 20S proteasomes, namely the immunoproteasome and the two intermediate proteasomes, might help cells to eliminate proteins containing disordered domains, including those induced by oxidative stress.
Ecological parameter reductions, environmental regimes, and characteristic process diagram of carbon dioxide fluxes in coastal salt marshes
Authors: Ishtiaq Khandker S. , Abdul-Aziz Omar I.
Published: September 2020

We investigated the ecological parameter reductions (termed “similitudes”) and characteristic patterns of the net uptake fluxes of carbon dioxide (CO2) in coastal salt marshes using dimensional analysis method from fluid mechanics and hydraulic engineering. Data collected during May–October, 2013 from four salt marshes in Waquoit Bay and adjacent estuary, Massachusetts, USA were utilized to evaluate the theoretically-derived dimensionless flux and various ecological driver numbers. Two meaningful dimensionless groups were discovered as the light use efficiency number (LUE = CO2 normalized by photosynthetically active radiation) and the biogeochemical number (combination of soil temperature, porewater salinity, and atmospheric pressure). A semi-logarithmic plot of the dimensionless numbers indicated the emergence of a characteristic diagram represented by three distinct LUE regimes (high, transitional, and low). The high regime corresponded to the most favorable (high temperature and low salinity) condition for CO2 uptake, whereas the low regime represented an unfavorable condition (low temperature and high salinity). The analysis identified two environmental thresholds (soil temperature ~ 17 °C and salinity ~ 30 ppt), which dictated the regime transitions of CO2 uptake. The process diagram and critical thresholds provide important insights into the CO2 uptake potential of coastal wetlands in response to changes in key environmental drivers.
Identification of volatile components from oviposition and non-oviposition plants of Gasterophilus pecorum (Diptera: Gasterophilidae)
Authors: Zhou Ran , Zhang Ke , Zhang Tiange , Zhou Tong , Chu Hongjun , Ge Yan , Wang Chen , Li Kai
Published: September 2020

Oviposition by Gasterophilus pecorum on shoot tips of Stipa caucasica is a key determinant of its severe infection of the reintroduced Przewalski’s horse (Equus przewalskii). Volatiles in shoots of grasses on which Przewalski’s horse feeds, including S. caucasica at preoviposition, oviposition, and postoviposition stages of G. pecorum, S. caucasica, Stipa orientalis, and Ceratoides latens at the oviposition stage, and S. caucasica in various growth periods, were collected by dynamic headspace adsorption and analyzed by automatic thermal desorption gas chromatography-mass spectrometry. Among five volatiles with highest relative contents under three sets of conditions, caprolactam and 3-hexen-1-ol,(Z)- were common to all samples. Caprolactam was highest in C. latens at oviposition stage of G. pecorum and lowest in S. caucasica at postoviposition stage, and that of 3-hexen-1-ol,(Z)- was lowest in C. latens and highest in S. caucasica at its oviposition stage. Particularly, in S. caucasica during the three oviposition phenological stages of G. pecorum, 3-hexen-1-ol,acetate,(Z)-, 2(5H)-furanone,5-ethyl-, and 3-hexen-1-ol,acetate,(E)- were unique, respectively, to the preoviposition, oviposition, and postoviposition stages; in three plant species during the oviposition stage of G. pecorum, 3-hexen-1-ol,acetate,(Z)-, 3-hexenal, and 1-hexanol were unique to S. orientalis, acetic acid, hexanal, and 2(5H)-furanone,5-ethyl- to S. caucasica, and 1,3,6-octatriene,3,7-dimethyl-, cis-3-hexenyl isovalerate, and acetic acid hexyl ester to C. latens; in S. caucasica, 2-undecanone,6,10-dimethyl- was unique to the early growth period, acetic acid and 2(5H)-furanone,5-ethyl- to the flourishing growth period, and 3-hexen-1-ol,acetate,(Z)- and 1,3,6-octatriene,3,7-dimethyl- to the late growth period. Furthermore, substances specific to S. orientalis and C. latens were also present in S. caucasica, except at oviposition stage. Our findings will facilitate studies on G. pecorum’s adaptation to the arid desert steppe and its future control.
Solvable delay model for epidemic spreading: the case of Covid-19 in Italy
Authors: Dell’Anna Luca
Published: September 2020

We study a simple realistic model for describing the diffusion of an infectious disease on a population of individuals. The dynamics is governed by a single functional delay differential equation, which, in the case of a large population, can be solved exactly, even in the presence of a time-dependent infection rate. This delay model has a higher degree of accuracy than that of the so-called SIR model, commonly used in epidemiology, which, instead, is formulated in terms of ordinary differential equations. We apply this model to describe the outbreak of the new infectious disease, Covid-19, in Italy, taking into account the containment measures implemented by the government in order to mitigate the spreading of the virus and the social costs for the population.
Impairment of synaptic plasticity and novel object recognition in the hypergravity-exposed rats
Authors: Lee Jinho , Jang Doohyeong , Jeong Hyerin , Kim Kyu-sung , Yang Sunggu
Published: September 2020

The gravity is necessary for living organisms to operate various biological events including hippocampus-related functions of learning and memory. Until now, it remains inconclusive how altered gravity is associated with hippocampal functions. It is mainly due to the difficulties in generating an animal model experiencing altered gravity. Here, we demonstrate the effects of hypergravity on hippocampus-related functions using an animal behavior and electrophysiology with our hypergravity animal model. The hypergravity (4G, 4 weeks) group showed impaired synaptic efficacy and long-term potentiation in CA1 neurons of the hippocampus along with the poor performance of a novel object recognition task. Our studies suggest that altered gravity affects hippocampus-related cognitive functions, presumably through structural and functional adaptation to various conditions of gravity shift.
Photoinduced spin dynamics in a uniaxial intermetallic heterostructure $$\hbox {TbCo}_2/\hbox {FeCo}$$
Authors: Ovcharenko Sergei , Gaponov Mikhail , Klimov Alexey , Tiercelin Nicolas , Pernod Philippe , Mishina Elena , Sigov Alexandr , Preobrazhensky Vladimir
Published: September 2020

Intermetallic heterostructures of rare-earth and transition metals exhibit physical properties prospective for various applications. These structures combine giant magnetostriction, controllable magnetic anisotropy, magneto-optical activity and allow spin reorientation transitions (SRT) induced by magnetic field at room temperature. Here, we present the results of a study of spin dynamics induced by ultrafast optical excitation in the $$\hbox {TbCo}_2\hbox {/FeCo}$$

TbCo
2

/FeCo

heterostructure. The time dependence of the light polarization rotation excited by a pump optical pulse with a duration of 35 fs was measured in the total range of the SRT created by external DC magnetic field. We found hysteretic dependence of the polarization rotation on magnetizing field that is specific for spin dynamics near SRT. Enhancement of the rotation is observed in the critical points of the SRT and near the points of magnetization switch from metastable to stable spin states. In the time-domain, two characteristic delays of 20 ps and 200 ps were found, corresponding to the maximum deviation of the light polarization after excitation. The first is explained by the precession motion of spins out of the plane of the structure. The latter is accounted for the spin in-plane deviation from its initial position and thermal relaxation of the anisotropy.
Protein metabolism and physical fitness are physiological determinants of body condition in Southern European carnivores
Authors: Santos Nuno , Nakamura Mónia , Rio-Maior Helena , Álvares Francisco , Barasona Jose Ángel , Rosalino Luís Miguel , Santos Maria João , Santos-Reis Margarida , Ferreras Pablo , Díaz-Ruiz Francisco , Monterroso Pedro
Published: September 2020

The physiological significance of biometric body condition indices (bBCI) is poorly understood. We hypothesized that bBCI are composite metrics of nutritional physiology, physical fitness and health. To test this hypothesis, we first compared the performance of eight bBCI, using 434 Southern European carnivores from six species as a model system; and then identified, by non-destructive methods, the hematology and serum biochemistry correlates of three selected bBCI. Fulton’s K Index, Major Axis Regression Residuals and Scaled Mass Index were the only bBCI insensitive to the effect of sex and age. The most informative physiological parameters in explaining the variation of these bBCI were the albumin (Effect Size (ES) = − 1.66 to − 1.76), urea (ES = 1.61 to 1.85) and total bilirubin (ES = − 1.62 to − 1.79). Hemoglobin and globulins (positive) and cholesterol (negative) were moderately informative (0.9 <|ES|< 1.5). This study shows that most bBCI do not control for the effect of age and sex in Southern European carnivores. Our results support that bBCI are composite measures of physiologic processes, reflecting a positive gradient from protein-poor to protein-rich diets, accompanied by increased physical fitness. Biometric body condition indices allow the integration of ecologically relevant physiological aspects in an easily obtained metric.
Breeding transients in capture–recapture modeling and their consequences for local population dynamics
Authors: Oro Daniel , Doak Daniel F.
Published: September 2020

Standard procedures for capture–mark–recapture modelling (CMR) for the study of animal demography include running goodness-of-fit tests on a general starting model. A frequent reason for poor model fit is heterogeneity in local survival among individuals captured for the first time and those already captured or seen on previous occasions. This deviation is technically termed a transience effect. In specific cases, simple, uni-state CMR modeling showing transients may allow researchers to assess the role of these transients on population dynamics. Transient individuals nearly always have a lower local survival probability, which may appear for a number of reasons. In most cases, transients arise due to permanent dispersal, higher mortality, or a combination of both. In the case of higher mortality, transients may be symptomatic of a cost of first reproduction. A few studies working at large spatial scales actually show that transients more often correspond to survival costs of first reproduction rather than to permanent dispersal, bolstering the interpretation of transience as a measure of costs of reproduction, since initial detections are often associated with first breeding attempts. Regardless of their cause, the loss of transients from a local population should lower population growth rate. We review almost 1000 papers using CMR modeling and find that almost 40% of studies fitting the searching criteria (N = 115) detected transients. Nevertheless, few researchers have considered the ecological or evolutionary meaning of the transient phenomenon. Only three studies from the reviewed papers considered transients to be a cost of first reproduction. We also analyze a long-term individual monitoring dataset (1988–2012) on a long-lived bird to quantify transients, and we use a life table response experiment (LTRE) to measure the consequences of transients at a population level. As expected, population growth rate decreased when the environment became harsher while the proportion of transients increased. LTRE analysis showed that population growth can be substantially affected by changes in traits that are variable under environmental stochasticity and deterministic perturbations, such as recruitment, fecundity of experienced individuals, and transient probabilities. This occurred even though sensitivities and elasticities of these parameters were much lower than those for adult survival. The proportion of transients also increased with the strength of density-dependence. These results have implications for ecological and evolutionary studies and may stimulate other researchers to explore the ecological processes behind the occurrence of transients in capture–recapture studies. In population models, the inclusion of a specific state for transients may help to make more reliable predictions for endangered and harvested species.
A new isolation device for shortening gene flow distance in small-scale transgenic maize breeding
Authors: Zhang Lili , Huo Shanshan , Cao Yang , Xie Xiang , Tan Yanhua , Zhang Yuliang , Zhao Hui , He Pingping , Guo Jingyuan , Xia Qiyu , Zhou Xia , Long Huan , Guo Anping
Published: September 2020

The transmission of pollen is the main cause of maize gene flow. Under the compulsory labeling system for genetically modified (GM) products in China, isolation measures are crucial. At present, there is no effective isolation device for preventing and controlling the short-range flow of GM maize pollen. The purposes of the present experiments were to overcome the deficiencies of existing technology and to demonstrate a new isolation device for decreasing the gene flow distance of GM maize. The isolation device we invented was shown to be more robust than traditional isolation methods, and it can be disassembled and repeatedly reused. The most important point was that the frequency of gene flow could be greatly reduced using this device. When the distance from the isolation device was more than 1 m, the gene flow rate could be decreased to less than 1%, and when the distance from the isolation device was more than 10 m, the gene flow rate could be reduced to less than 0.1%. When the isolation device was adopted to isolate GM maize in conjunction with bagging the tassels of GM maize at the pollination stage, the gene flow could be controlled to less than 0.1% when the distance from the isolation device was more than 1 m. This device was, however, only applicable for small plots and can shorten the isolation distance of GM maize planting and improve the purity of seeds, all while meeting the needs of close isolation breeding. The use of this device represents a feasible method for risk prevention and control of GM crops.
Metagenomic analysis and identification of emerging pathogens in blood from healthy donors
Authors: Xu Min , Gao Jing , Li Shilin , Zeng Min , Wu Jianming , Luo Mao
Published: September 2020

Emerging infectious pathogens that threaten blood transfusions are known to be present in blood samples from healthy/qualified donors. The objective of this study was to investigate the microbiome of blood from healthy donors from the Luzhou area in southwestern China. Potential pathogens and cytomegalovirus (CMV) infection in the donor blood were identified. Total plasma nucleic acids were extracted from one pool of 5734 samples and were constructed for metagenomics analysis using Illumina sequencing. The microbiome and potential emerging/re-emerging pathogens were identified using bioinformatics analysis. Moreover, CMV antigen was measured via an enzyme-linked immunosorbent assay, and the CMV DNA level was assessed by quantitative RT-PCR. A total of 132 bacterial reads, 65 viral reads and 165 parasitic reads were obtained. The most frequent bacterium was Escherichia coli (95/132, 72%) with 95 reads in 132 bacterial reads, and the most prevalent parasite was Toxoplasma gondii (131/165, 79%). Among the viruses, cytomegalovirus (44/65, 68%) accounted for the highest frequency, followed by Hepatitis E Virus (10/65, 15%). Moreover, the positive rate of CMV-IgG was 46.25% (2652/5734), and the positive rate of CMV-IgM was 5.82% (334/5734). The positive rate of dual positive (IgG+ and IgM+) CMV was 0.07% (4/5734). Twenty-one (0.37%) specimens from 5734 donated blood samples were positive for CMV DNA. The CMV DNA levels ranged from 7.56 × 102 to 3.58 × 103 copies/mL. The current study elucidated the microbiome structure in blood from healthy/qualified donors in the Luzhou area and identified emerging/re-emerging pathogens. This preliminary study contributes to information regarding blood transfusion safety in China.
HLA-G and HLA-F protein isoform expression in breast cancer patients receiving neoadjuvant treatment
Authors: Wuerfel Franziska M. , Huebner Hanna , Häberle Lothar , Gass Paul , Hein Alexander , Jud Sebastian M. , Hack Carolin C. , Wunderle Marius , Schulz-Wendtland Rüdiger , Erber Ramona , Hartmann Arndt , Ekici Arif B. , Beckmann Matthias W. , Fasching Peter A. , Ruebner Matthias
Published: September 2020

The immunosuppressive human leukocyte antigens HLA-G and HLA-F are expressed on trophoblast and malignant cells. Four membrane-bound and three soluble HLA-G protein isoforms have been described, which have different immunosuppressive potentials. HLA-F has three transcript variants, resulting in three different protein isoforms. The aim of this study was to evaluate the prognostic and predictive value of HLA-G and HLA-F protein isoform expression patterns in patients with breast cancer. Core biopsies were taken at diagnosis in patients with HER2+ (n = 28), luminal B-like (n = 49) and triple-negative (n = 38) breast cancers who received neoadjuvant chemotherapy. Expression levels of HLA-F and -G were correlated with the pathological complete response (pCR). Protein expression was determined by Western blot analysis, using two antibodies for each HLA, specific for different isoforms. The protein expression of HLA isoforms did not significantly differ between breast cancer subtypes. However, some initial indications were found for an association between the soluble HLA-G6 protein isoform and pCR in HER2+ breast cancer. The study provides preliminary evidence for the evaluation of HLA-G isoform expression, in particular HLA-G6, as a possible new marker for pCR in HER2+ breast cancer.
Myh11+ microvascular mural cells and derived mesenchymal stem cells promote retinal fibrosis
Authors: Ray H. Clifton , Corliss Bruce A. , Bruce Anthony C. , Kesting Sam , Dey Paromita , Mansour Jennifer , Seaman Scott A. , Smolko Christian M. , Mathews Corbin , Dey Bijan K. , Owens Gary K. , Peirce Shayn M. , Yates Paul A.
Published: September 2020

Retinal diseases are frequently characterized by the accumulation of excessive scar tissue found throughout the neural retina. However, the pathophysiology of retinal fibrosis remains poorly understood, and the cell types that contribute to the fibrotic response are incompletely defined. Here, we show that myofibroblast differentiation of mural cells contributes directly to retinal fibrosis. Using lineage tracing technology, we demonstrate that after chemical ocular injury, Myh11+ mural cells detach from the retinal microvasculature and differentiate into myofibroblasts to form an epiretinal membrane. Inhibition of TGFβR attenuates Myh11+ retinal mural cell myofibroblast differentiation, and diminishes the subsequent formation of scar tissue on the surface of the retina. We demonstrate retinal fibrosis within a murine model of oxygen-induced retinopathy resulting from the intravitreal injection of adipose Myh11-derived mesenchymal stem cells, with ensuing myofibroblast differentiation. In this model, inhibiting TGFβR signaling does not significantly alter myofibroblast differentiation and collagen secretion within the retina. This work shows the complexity of retinal fibrosis, where scar formation is regulated both by TGFβR and non-TGFβR dependent processes involving mural cells and derived mesenchymal stem cells. It also offers a cautionary note on the potential deleterious, pro-fibrotic effects of exogenous MSCs once intravitreally injected into clinical patients.
Differential expression of genes in olive leaves and buds of ON- versus OFF-crop trees
Authors: Dastkar Ebrahim , Soleimani Ali , Jafary Hossein , de Dios Alche Juan , Bahari Abbas , Zeinalabedini Mehrshad , Salami Seyed Alireza
Published: September 2020

Alternate bearing (AB) refers to the tendency of trees to have an irregular crop load from 1 year (ON) to the next year (OFF). Despite its economic importance, it is not fully understood how gene networks and their related metabolic pathways may influence the irregular bearing in olive trees. To unravel molecular mechanisms of this phenomenon in olive (cv. Conservalia), the whole transcriptome of leaves and buds from ON and OFF-trees was sequenced using Illumina next generation sequencing approach. The results indicated that expressed transcripts were involved in metabolism of carbohydrates, polyamins, phytohormones and polyphenol oxidase (POD) related to antioxidant system. Expression of POD was increased in leaf samples of ON- versus OFF-trees. The expression pattern of the greater number of genes was changed more in buds than in leaves. Up-regulation of gene homologues to the majority of enzymes that were involved in photorespiration metabolism pathway in buds of ON-trees was remarkable that may support the hypotheses of an increase in photorespiratory metabolism in these samples. The results indicated changes in expression pattern of homologous to those taking part of abscisic acid and cytokinin synthesis which are connected to photorespiration. Our data did not confirm expression of homologue (s) to those of chlorogenic acid metabolism, which has been addressed earlier that have a probable role in biennial bearing in olive. Current findings provide new candidate genes for further functional analysis, gene cloning and exploring of molecular basses of AB in olive.
Behavioral effects induced by organic insecticides can be exploited for a sustainable control of the Orange Spiny Whitefly Aleurocanthus spiniferus
Authors: Mokrane Selma , Cavallo Giuseppe , Tortorici Francesco , Romero Elena , Fereres Alberto , Djelouah Khaled , Verrastro Vincenzo , Cornara Daniele
Published: September 2020

The Orange Spiny Whitefly (OSW)Aleurocanthus spiniferus(Hemiptera: Aleyrodidae) represents a new serious threat toCitrusspp., grapevine and ornamental plants in the whole Mediterranean area. Such threat urgently calls for the development of a sustainable control strategy, including insecticides compatible with biological control, and applicable also in organic citrus farming that represent an essential part of Mediterranean agricultural economy. Therefore, we evaluated the toxicity and the effects on host searching, oviposition, and probing and feeding behavior exerted on OSW by organic insecticides supposed to have limited side effects on environment and ecosystem services, i.e. sweet orange essential oil (EO), extract ofClitoria ternatea(CT), mineral oil, pyrethrin and azadirachtin. Despite none of the compounds caused a significant mortality of any of the OSW instars, we observed interesting effects on whitefly behavior: (i) EO and pyrethrin showed a relevant repellent effect, with impairment of both adults landing and oviposition on treated plants; (ii) CT and pyrethrin strongly affected probing behavior. Here, in the light of our findings, we discuss possible OSW sustainable control strategies and further research perspectives.
Trinuclear Cd3O14 hexaborate and two nickel borates based on molten salt synthesis and precursor synthesis: structure, characterization, and properties
Authors: He Yong , Liu Ying , Xin Shu-Sheng , Pan Chun-Yang
Published: September 2020

Different synthesis strategies were applied in this work to prepare metal borates; three borates including Cd3[B6O9(OH)2]2·2NO3·4H2O (1), Ni0.8Mn0.2{B6O7(OH)3[O(CH2)2NH2]3} (2), and [Ni(1-MI)6]·[B5O6(OH)4]2·2DMF (3) were successfully prepared.
A highly efficient electrochemical oxygen evolution reaction catalyst constructed from a S-treated two-dimensional Prussian blue analogue
Authors: Wang Jinlei , Zhang Meilin , Li Jinhui , Jiao Feixiang , Lin Yu , Gong Yaqiong
Published: September 2020

A synthesized S-CoFe-PBA/CFP electrode exhibited remarkable electrocatalytic performance and durability toward the OER under alkaline conditions.
A review of phosphate adsorption on Mg-containing materials: kinetics, equilibrium, and mechanistic insights
Authors: Silva Manoj , Baltrusaitis Jonas
Published: September 2020

This tutorial review highlights the relationships between the fundamental studies of kinetics, equilibrium, and mechanism of phosphate adsorption.
Lactobacillus fermentum KP-3-fermented ginseng ameliorates alcohol-induced liver disease in C57BL/6N mice through the AMPK and MAPK pathways
Authors: You Ying , Liu Yan-long , Ai Zhi-Yi , Wang Yu-Shan , Liu Jun-Mei , Piao Chun-Hong , Wang Yu-Hua
Published: September 2020

L. fermentum KP-3-fermented ginseng ameliorates ALD in mice through the AMPK and MAPK pathways.
Morphology-controlled MoS2 by low-temperature atomic layer deposition
Authors: Shen Chengxu , Raza Muhammad Hamid , Amsalem Patrick , Schultz Thorsten , Koch Norbert , Pinna Nicola
Published: September 2020

Morphologies-controlled MoS2 deposited by low temperature ALD exhibit tunable optical properties.
Synthesis of α-aminooxy amides through [3 + 3] cycloaddition and Sc(OTf)3-catalyzed double C–N bond cleavage in a one-pot reaction
Authors: Luo Yan , Chen Chun-Hua , Zhu Fan , Mo Dong-Liang
Published: September 2020

A [3 + 3] cycloaddition and Sc(OTf)3-catalyzed double C–N bond cleavage to synthesize various α-aminooxy amides bearing a quaternary carbon in one pot have been achieved from N-vinyl nitrones and α-bromohydroxamates.
Bioinspired structural color nanocomposites with healable capability
Authors: Zhang Lianbin , Li Miaomiao , Lyu Quanqian , Zhu Jintao
Published: September 2020

This minireview summarizes the recent development of healable structural color nanocomposites from the perspective of the construction strategies.
Optimization of double-vortex-assisted matrix solid-phase dispersion for the rapid determination of paraben preservative residues in leafy vegetables
Authors: Yang Chun-Ju , Chung Wu-Hsun , Ding Wang-Hsien
Published: September 2020

A rapid and simply DVA-MSPD coupled UHPLC-ESI(−)-QToF-MS was developed to determine parabens residues in leafy vegetable samples.
Photocontrol of CRISPR/Cas9 function by site-specific chemical modification of guide RNA
Authors: Wang Yang , Liu Yan , Xie Fan , Lin Jiao , Xu Liang
Published: September 2020

The CRISPR/Cas9 function is optically controlled in living cells by the site-specifically caged guide RNA based on the RNA–protein interaction.
Single-emissive-layer all-perovskite white light-emitting diodes employing segregated mixed halide perovskite crystals
Authors: Yu Hongling , Wang Heyong , Pozina Galia , Yin Chunyang , Liu Xiao-Ke , Gao Feng
Published: September 2020

We demonstrated a single-emissive-layer all-perovskite white light-emitting diode based on a mixed halide perovskite film.
Charging-driven coarsening and melting of a colloidal nanoparticle monolayer at an ionic liquid–vacuum interface
Authors: Bischak Connor G. , Raybin Jonathan G. , Kruppe Jonathon W. , Ginsberg Naomi S.
Published: September 2020

We induce and investigate the coarsening and melting dynamics of an initially static nanoparticle colloidal monolayer at an ionic liquid–vacuum interface, driven by a focused, scanning electron beam.
Longitudinal Decline on the Dichotic Digits Test
Authors: Dillard Lauren K. , Fischer Mary E. , Pinto Alex , Klein Barbara E. K. , Paulsen Adam J. , Schubert Carla R. , Tsai Michael Y. , Tweed Theodore S. , Cruickshanks Karen J.
Published: September 2020

Purpose

The dichotic digits test (DDT) is commonly administered in clinical and research settings, but it is not well understood how performance changes in aging. The purpose of this study is to determine the 5-year change on the free recall task and right ear advantage (REA) in a population-based cohort and factors associated with change.

Method

Participants in the population-based Epidemiology of Hearing Loss Study, who completed the DDT during the fourth (2009–2010) and fifth (2013–2016) examination periods were included (n= 865,Mage= 72.8 years at baseline). Free recall DDT was administered using 25 sets of triple-digit pairs presented at 70 dB HL. The REA was calculated by subtracting the score in the left ear from the score in the right ear.

Results

In 5 years, most participants (62.4%) declined on free recall performance (mean decline = 3.0% [4.5 digits],p< .01). In age-sex–adjusted models, higher baseline scores, hearing impairment, and lower education were significantly associated with increased risk of decline. An REA at baseline (76.8%) and follow-up (77.9%) was common. Half of participants (50.6%) had a 5-year REA widening (M= 1.9% [1.4 digits],p= .01). Older age, but not hearing impairment, was associated with increased risk of REA widening.

Conclusions

The 5-year decline on free recall recognition performance was not associated with age but was associated with hearing impairment, whereas the 5-year widening of REA was associated with age but not hearing impairment. These results indicate that the REA may be a more sensitive measure of aging of the central auditory system than free recall performance.