bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends in the molecular epidemiology and population genetics of emergingSporothrixspecies
Authors: Roberto T.N. , de Carvalho J.A. , Beale M.A. , Hagen F. , Fisher M.C. , Hahn R.C. , de Camargo Z.P. , Rodrigues A.M. 
Published: December 2021

Paracoccidioidomycosis (PCM) is a life-threatening systemic fungal infection acquired after inhalation ofParacoccidioidespropagules from the environment. The main agents include members of theP. brasiliensiscomplex (phylogenetically-defined species S1, PS2, PS3, and PS4) andP. lutzii. DNA-sequencing of protein-coding loci (e.g.,GP43,ARF, andTUB1) is the reference method for recognizingParacoccidioidesspecies due to a lack of robust phenotypic markers. Thus, developing new molecular markers that are informative and cost-effective is key to providing quality information to explore genetic diversity withinParacoccidioides. We report using new amplified fragment length polymorphism (AFLP) markers and mating-type analysis for genotypingParacoccidioidesspecies. The bioinformatic analysis generated 144in silicoAFLP profiles, highlighting two discriminatory primer pairs combinations (#1 EcoRI-AC/MseI-CT and #2 EcoRI-AT/MseI-CT). The combinations #1 and #2 were usedin vitroto genotype 165Paracoccidioidesisolates recovered from across a vast area of South America. Considering the overall scored AFLP markersin vitro(67-87 fragments), the values of polymorphism information content (PIC= 0.3345-0.3456), marker index (MI= 0.0018), effective multiplex ratio (E= 44.6788-60.3818), resolving power (Rp= 22.3152-34.3152), discriminating power (D= 0.5183-0.5553), expected heterozygosity (H= 0.4247-0.4443), and mean heterozygosity (H<inf>avp</inf> = 0.00002-0.00004), demonstrated the utility of AFLP markers to speciateParacoccidioidesand to dissect both deep and fine-scale genetic structures. Analysis of molecular variance (AMOVA) revealed that the total genetic variance (65-66 %) was due to variability amongP. brasiliensiscomplex andP. lutzii(PhiPT = 0.651-0.658,P < 0.0001), supporting a highly structured population. Heterothallism was the exclusive mating strategy, and the distributions ofMAT1-1orMAT1-2idiomorphs were not significantly skewed (1:1 ratio) forP. brasiliensis s. str.(χ2= 1.025;P= 0.3113),P. venezuelensis(χ2= 0.692;P= 0.4054), andP. lutzii(χ2= 0.027;P= 0.8694), supporting random mating within each species. In contrast, skewed distributions were found forP. americana(χ2= 8.909;P= 0.0028) andP. restrepiensis(χ2= 4.571;P= 0.0325) with a preponderance ofMAT1-1. Geographical distributions confirmed thatP. americana,P. restrepiensis, andP. lutziiare more widespread than previously thought.P. brasiliensis s. str.is by far the most widely occurring lineage in Latin America countries, occurring in all regions of Brazil. Our new DNA fingerprint assay proved to be rapid, reproducible, and highly discriminatory, to give insights into the taxonomy, ecology, and epidemiology ofParacoccidioidesspecies, guiding disease-control strategies to mitigate PCM.
COMPARING ANALYSIS OF PRETREATMENT METHODS OF WOOD AND BONE MATERIALS FOR THE CHRONOLOGY OF PERIPHERAL BURIALS AT TUNNUG 1, TUVA REPUBLIC, RUSSIA
Authors: Pawełczyk Fatima , Hajdas Irka , Sadykov Timur , Blochin Jegor , Caspari Gino 
Published: December 2021

ABSTRACTNine burials from Tunnug 1 site in Tuva Republic, which contained human and animal bones as well as remains of wood, were chosen for intercomparison study of preparation methods. Nine human bones, nine animal bones and 11 pieces of wood were prepared. Gelatin extracted from bones was purified using the UF method but the extraction from bones was modified with respect to acid and base treatment. Wood samples were treated as whole using acid-base-acid and cellulose was extracted for comparison. The results confirmed a highly consistent chronology of the sites centered at 200–400 CE, however, a few bones resulted in an offset between ages obtained by different methods. The extraction of cellulose was limited due to the poor preservation of wood. Our results highlight problems of dating poorly preserved bones and wood.
Probing Ferroelectric Behavior in Sub-10 nm Bismuth-Rich Aurivillius Films by Piezoresponse Force Microscopy
Authors: Keeney Lynette , Colfer Louise , Schmidt Michael 
Published: December 2021

Abstract
Sub-10 nm ferroelectric and multiferroic materials are attracting increased scientific and technological interest, owing to their exciting physical phenomena and prospects in miniaturized electronic devices, neuromorphic computing, and ultra-compact data storage. The Bi6Ti2.9Fe1.5Mn0.6O18 (B6TFMO) Aurivillius system is a rare example of a multiferroic that operates at room temperature. Since the formation of magnetic impurity phases can complicate attempts to measure ferromagnetic signal intrinsic to the B6TFMO multiferroic phase and thus limits its use, herein we minimize this by utilizing relatively large (49%) bismuth excess to counteract its volatility during sub-10 nm growth. X-ray diffraction, electron microscopy, and atomic force microscopy show sample crystallinity and purity are substantially improved on increasing bismuth excess from 5 to 49%, with the volume fraction of surface impurities decreasing from 2.95–3.97 vol% down to 0.02–0.31 vol%. Piezoresponse force microscopy reveals 8 nm B6TFMO films are ferroelectric, with an isotropic random distribution of stable in-plane domains and weaker out-of-plane piezoresponse. By reducing the volume fraction of magnetic impurities, this work demonstrates the recent progress in the optimization of ultra-thin B6TFMO for future multiferroic technologies. We show how the orientation of the ferroelectric polarization can be switched in 8 nm B6TFMO and arrays can be “written” and “read” to express states permitting anti-parallel information storage.
Moisture Fluctuations Modulate Abiotic and Biotic Limitations of H2 Soil Uptake
Authors: Bertagni Matteo B. , Paulot Fabien , Porporato Amilcare 
Published: December 2021

AbstractSoil uptake by H2‐oxidizing bacteria is the main sink of the global hydrogen cycle, accounting for nearly 80% of the atmospheric H2 consumption. Although the H2 uptake is strongly influenced by soil moisture, little attention has been paid to coherently couple the water and hydrogen dynamics in soils. Toward this goal, we improve the mechanistic representation of the H2 uptake as a function of soil moisture and highlight the role of the moisture temporal fluctuations on the biotic consumption of H2. The results show that, due to the strongly nonlinear relationship between soil moisture and H2 uptake, addressing the dry‐wet sequences is necessary to characterize the H2 uptake in semi‐arid regions correctly. From novel analytical relationships validated with field data, we also infer the biotic and abiotic limitations in the global soil H2 uptake. It is shown that, diffusion generally limits the uptake in humid temperate and tropical regions, while biotic limitations tend to occur in very arid or cold soils. Finally, we discuss the implications that climate change may have on the H2 soil sink.
SETD5 modulates homeostasis of hematopoietic stem cells by mediating RNA Polymerase II pausing in cooperation with HCF-1
Authors: Li Mengke , Qiu Chen , Bian Yujie , Shi Deyang , Wang Bichen , Ma Qiuyi , Wang Xiaomin , Shi Jun , Zhang Lianfeng , Ma Yuanwu , Zhu Ping , Cheng Tao , Chu Yajing , Yuan Weiping 
Published: December 2021

AbstractSETD5mutations were identified as the genetic causes of neurodevelopmental disorders. While the whole-body knockout ofSetd5in mice leads to embryonic lethality, the role of SETD5 in adult stem cell remains unexplored. Here, a critical role ofSetd5in hematopoietic stem cells (HSCs) is identified. Specific deletion ofSetd5in hematopoietic system significantly increased the number of immunophenotypic HSCs by promoting HSC proliferation.Setd5-deficient HSCs exhibited impaired long-term self-renewal capacity and multiple-lineage differentiation potentials under transplantation pressure. Transcriptome analysis ofSetd5-deficient HSCs revealed a disruption of quiescence state of long-term HSCs, a cause of the exhaustion of functional HSCs. Mechanistically, SETD5 was shown to regulate HSC quiescence by mediating the release of promoter-proximal paused RNA polymerase II (Pol II) on E2F targets in cooperation with HCF-1 and PAF1 complex. Taken together, these findings reveal an essential role of SETD5 in regulating Pol II pausing-mediated maintenance of adult stem cells.
Hematopoiesis and innate immunity: an inseparable couple for good and bad times, bound together by an hormetic relationship
Authors: Ratajczak Mariusz Z. , Kucia Magdalena 
Published: December 2021

AbstractHematopoietic and immune cells originate from a common hematopoietic/lymphopoietic stem cell what explains that these different cell types often share the same receptors and respond to similar factors. Moreover, the common goal of both lineages is to ensure tissue homeostasis under steady-state conditions, fight invading pathogens, and promote tissue repair. We will highlight accumulating evidence that innate and adaptive immunity modulate several aspects of hematopoiesis within the hormetic zone in which the biological response to low exposure to potential stressors generally is favorable and benefits hematopoietic stem/progenitor cells (HSPCs). Innate immunity impact on hematopoiesis is pleiotropic and involves both the cellular arm, comprised of innate immunity cells, and the soluble arm, whose major component is the complement cascade (ComC). In addition, several mediators released by innate immunity cells, including inflammatory cytokines and small antimicrobial cationic peptides, affect hematopoiesis. There are intriguing observations that HSPCs and immune cells share several cell-surface pattern-recognition receptors (PRRs), such as Toll-like receptors (TLRs) and cytosol-expressed NOD, NOD-like, and RIG-I-like receptors and thus can be considered “pathogen sensors”. In addition, not only lymphocytes but also HSPCs express functional intracellular complement proteins, defined as complosome which poses challenging questions for further investigation of the intracellular ComC-mediated intracrine regulation of hematopoiesis.
Predation increases multiple components of microbial diversity in activated sludge communities
Authors: Burian Alfred , Pinn Daisy , Peralta-Maraver Ignacio , Sweet Michael , Mauvisseau Quentin , Eyice Ozge , Bulling Mark , Röthig Till , Kratina Pavel 
Published: December 2021

Abstract
Protozoan predators form an essential component of activated sludge communities that is tightly linked to wastewater treatment efficiency. Nonetheless, very little is known how protozoan predation is channelled via bacterial communities to affect ecosystem functioning. Therefore, we experimentally manipulated protozoan predation pressure in activated-sludge communities to determine its impacts on microbial diversity, composition and putative functionality. Different components of bacterial diversity such as taxa richness, evenness, genetic diversity and beta diversity all responded strongly and positively to high protozoan predation pressure. These responses were non-linear and levelled off at higher levels of predation pressure, supporting predictions of hump-shaped relationships between predation pressure and prey diversity. In contrast to predation intensity, the impact of predator diversity had both positive (taxa richness) and negative (evenness and phylogenetic distinctiveness) effects on bacterial diversity. Furthermore, predation shaped the structure of bacterial communities. Reduction in top-down control negatively affected the majority of taxa that are generally associated with increased treatment efficiency, compromising particularly the potential for nitrogen removal. Consequently, our findings highlight responses of bacterial diversity and community composition as two distinct mechanisms linking protozoan predation with ecosystem functioning in activated sludge communities.
Loss of DSTYK activates Wnt/β-catenin signaling and glycolysis in lung adenocarcinoma
Authors: Zhong Chenxi , Chen Ming , Chen Yu , Yao Feng , Fang Wentao 
Published: December 2021

AbstractAberrant activation of Wnt/β-catenin signaling and dysregulation of metabolism have been frequently observed in lung cancer. However, the molecular mechanism by which Wnt/β-catenin signaling is regulated and the link between Wnt/β-catenin signaling and cancer metabolism are not fully understood. In this study, we showed that the loss of dual serine/threonine tyrosine protein kinase (DSTYK) led to the activation of Wnt/β-catenin signaling and upregulation of its target gene, lactate dehydrogenase (LDHA), and thus the elevation of lactate. DSTYK phosphorylated the N-terminal domain of β-catenin and inhibited Wnt/β-catenin signaling, which led to the inhibition of cell growth, colony formation and tumorigenesis in a lung adenocarcinoma mouse model. DSTYK was downregulated in lung cancer tissues, and its expression was positively correlated with the survival of patients with lung adenocarcinoma. Taken together, these results demonstrate that the loss of DSTYK activates Wnt/β-catenin/LDHA signaling to promote the tumorigenesis of lung cancer and that DSTYK may be a therapeutic target.
Defense responses of arbuscular mycorrhizal fungus-colonized poplar seedlings against gypsy moth larvae: a multiomics study
Authors: Jiang Dun , Tan Mingtao , Wu Shuai , Zheng Lin , Wang Qing , Wang Guirong , Yan Shanchun 
Published: December 2021

AbstractArbuscular mycorrhizal (AM) fungi may help protect plants against herbivores; however, their use for the pest control of woody plants requires further study. Here, we investigated the effect of Glomus mosseae colonization on the interactions between gypsy moth larvae and Populus alba × P. berolinensis seedlings and deciphered the regulatory mechanisms underlying the mycorrhizal-induced resistance in the leaves of mycorrhizal poplar using RNA-seq and nontargeted metabolomics. The resistance assay showed that AM fungus inoculation protected poplar seedlings against gypsy moth larvae, as evidenced by the decreased larval growth and reduced larval survival. A transcriptome analysis revealed that differentially expressed genes (DEGs) were involved in jasmonic acid biosynthesis (lipoxygenase, hydroperoxide dehydratase, and allene oxide cyclase) and signal transduction (jasmonate-ZIM domain and transcription factor MYC2) and identified the genes that were upregulated in mycorrhizal seedlings. Except for chalcone synthase and anthocyanidin synthase, which were downregulated in mycorrhizal seedlings, all DEGs related to flavonoid biosynthesis were upregulated, including 4-coumarate-CoA ligase, chalcone isomerase, flavanone 3-hydroxylase, flavonol synthase, and leucoanthocyanidin reductase. The metabolome analysis showed that several metabolites with insecticidal properties, including coumarin, stachydrine, artocarpin, norizalpinin, abietic acid, 6-formylumbelliferone, and vanillic acid, were significantly accumulated in the mycorrhizal seedlings. These findings suggest the potential of mycorrhiza-induced resistance for use in pest management of woody plants and demonstrate that the priming of JA-dependent responses in poplar seedlings contributes to mycorrhiza-induced resistance to insect pests.
A novel transcription factor CmMYB012 inhibits flavone and anthocyanin biosynthesis in response to high temperatures in chrysanthemum
Authors: Zhou Li-Jie , Geng Zhiqiang , Wang Yuxi , Wang Yiguang , Liu Shenhui , Chen Chuwen , Song Aiping , Jiang Jiafu , Chen Sumei , Chen Fadi 
Published: December 2021

AbstractFlavones are among the major colorless pigments synthesized through branches of the flavonoid pathway in plants. However, due to the absence of a gene encoding flavone synthase (FNS) in the model plant Arabidopsis thaliana species, the regulatory mechanism of FNS-catalyzed flavone biosynthesis has rarely been studied in plants. Here, it was found that flavones play a predominant role in the elimination of excess reactive oxygen species (ROS) at high temperatures in colorless plant organs. A novel atypical subgroup 7 (SG7) R2R3-MYB transcription factor, CmMYB012, was found to be induced in response to prolonged high temperatures and to inhibit flavone biosynthesis by directly regulating CmFNS. Moreover, CmMYB012 was also found to inhibit anthocyanin biosynthesis by suppressing the expression of CmCHS, CmDFR, CmANS, and CmUFGT. CmMYB012 overexpression exerted a negative influence on plant fitness and pink flower color formation, while CmMYB012 suppression had the opposite effect in response to high temperatures. Our findings provide new insights into the mechanisms by which high temperatures regulate the metabolism of flavones and anthocyanins to affect plant fitness and flower color formation.
Functions of silicon in plant drought stress responses
Authors: Wang Min , Wang Ruirui , Mur Luis Alejandro Jose , Ruan Jianyun , Shen Qirong , Guo Shiwei 
Published: December 2021

AbstractSilicon (Si), the second most abundant element in Earth’s crust, exerts beneficial effects on the growth and productivity of a variety of plant species under various environmental conditions. However, the benefits of Si and its importance to plants are controversial due to differences among the species, genotypes, and the environmental conditions. Although Si has been widely reported to alleviate plant drought stress in both the Si-accumulating and nonaccumulating plants, the underlying mechanisms through which Si improves plant water status and maintains water balance remain unclear. The aim of this review is to summarize the morphoanatomical, physiological, biochemical, and molecular processes that are involved in plant water status that are regulated by Si in response to drought stress, especially the integrated modulation of Si-triggered drought stress responses in Si accumulators and intermediate- and excluder-type plants. The key mechanisms influencing the ability of Si to mitigate the effects of drought stress include enhancing water uptake and transport, regulating stomatal behavior and transpirational water loss, accumulating solutes and osmoregulatory substances, and inducing plant defense- associated with signaling events, consequently maintaining whole-plant water balance. This study evaluates the ability of Si to maintain water balance under drought stress conditions and suggests future research that is needed to implement the use of Si in agriculture. Considering the complex relationships between Si and different plant species, genotypes, and the environment, detailed studies are needed to understand the interactions between Si and plant responses under stress conditions.
Disruption of the bHLH transcription factor Abnormal Tapetum 1 causes male sterility in watermelon
Authors: Zhang Ruimin , Chang Jingjing , Li Jiayue , Lan Guangpu , Xuan Changqing , Li Hao , Ma Jianxiang , Zhang Yong , Yang Jianqiang , Tian Shujuan , Yuan Li , Zhang Xian , Wei Chunhua 
Published: December 2021

Abstract
Although male sterility has been identified as a useful trait for hybrid vigor utilization and hybrid seed production, its underlying molecular mechanisms in Cucurbitaceae species are still largely unclear. Here, a spontaneous male-sterile watermelon mutant, Se18, was reported to have abnormal tapetum development, which resulted in completely aborted pollen grains. Map-based cloning demonstrated that the causal gene Citrullus lanatus Abnormal Tapetum 1 (ClATM1) encodes a basic helix-loop-helix (bHLH) transcription factor with a 10-bp deletion and produces a truncated protein without the bHLH interaction and functional (BIF) domain in Se18 plants. qRT–PCR and RNA in situ hybridization showed that ClATM1 is specifically expressed in the tapetum layer and in microsporocytes during stages 6–8a of anther development. The genetic function of ClATM1 in regulating anther development was verified by CRISPR/Cas9-mediated mutagenesis. Moreover, ClATM1 was significantly downregulated in the Se18 mutant, displaying a clear dose effect at the transcriptional level. Subsequent dual-luciferase reporter, β-glucuronidase (GUS) activity, and yeast one-hybrid assays indicated that ClATM1 could activate its own transcriptional expression through promoter binding. Collectively, ClATM1 is the first male sterility gene cloned from watermelon, and its self-regulatory activity provides new insights into the molecular mechanism underlying anther development in plants.
Transcriptome analysis in LRRK2 and idiopathic Parkinson’s disease at different glucose levels
Authors: Fernández-Santiago Rubén , Esteve-Codina Anna , Fernández Manel , Valldeoriola Francesc , Sanchez-Gómez Almudena , Muñoz Esteban , Compta Yaroslau , Tolosa Eduardo , Ezquerra Mario , Martí María J. 
Published: December 2021

AbstractType-2 diabetes (T2D) and glucose metabolic imbalances have been linked to neurodegenerative diseases, including Parkinson’s disease (PD). To detect potential effects of different glucose levels on gene expression, by RNA-seq we analyzed the transcriptome of dermal fibroblasts from idiopathic PD (iPD) patients, LRRK2-associated PD (L2PD) patients, and healthy controls (total n = 21 cell lines), which were cultured at two different glucose concentrations (25 and 5 mM glucose). In PD patients we identified differentially expressed genes (DEGs) that were related to biological processes mainly involving the plasmatic cell membrane, the extracellular matrix, and also neuronal functions. Such pathway deregulation was largely similar in iPD or L2PD fibroblasts. Overall, the gene expression changes detected in this study were associated with PD independently of glucose concentration.
Quantum generative adversarial networks with multiple superconducting qubits
Authors: Huang Kaixuan , Wang Zheng-An , Song Chao , Xu Kai , Li Hekang , Wang Zhen , Guo Qiujiang , Song Zixuan , Liu Zhi-Bo , Zheng Dongning , Deng Dong-Ling , Wang H. , Tian Jian-Guo , Fan Heng 
Published: December 2021

AbstractGenerative adversarial networks are an emerging technique with wide applications in machine learning, which have achieved dramatic success in a number of challenging tasks including image and video generation. When equipped with quantum processors, their quantum counterparts—called quantum generative adversarial networks (QGANs)—may even exhibit exponential advantages in certain machine learning applications. Here, we report an experimental implementation of a QGAN using a programmable superconducting processor, in which both the generator and the discriminator are parameterized via layers of single- and two-qubit quantum gates. The programmed QGAN runs automatically several rounds of adversarial learning with quantum gradients to achieve a Nash equilibrium point, where the generator can replicate data samples that mimic the ones from the training set. Our implementation is promising to scale up to noisy intermediate-scale quantum devices, thus paving the way for experimental explorations of quantum advantages in practical applications with near-term quantum technologies.