bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of straw returning with potassium fertilizer on the stem lodging resistance, grain quality and yield of spring maize (Zea mays L.)
Authors: Fan Ya-fang , Gao Ju-lin , Sun Ji-ying , Liu Jian , Su Zhi-jun , Hu Shu-ping , Wang Zhi-gang , Yu Xiao-fang 
Published: April 2021

AbstractThe effects of straw returning with potassium fertilizer on the stem lodging resistance, grain quality and yield of spring maize were investigated to provide a scientific basis for the rational utilization of Inner Mongolia spring maize straw and potassium fertilizer resources. This study utilized Xianyu 335 as the test material, and a split plot design was carried out in three ecological regions from eastern to western Inner Mongolia (Tumochuan Plain irrigation area, Hetao Plain irrigation area and Lingnan warm dry zone), with the straw returning method as the main plot and potassium fertilizer dosage as the subplot. The stem resistance index, grain quality and yield were systematically identified. Both application of potassium fertilizer and straw returning improved the resistance and yield indicators of spring maize. Straw returning increased the effectiveness of potassium fertilizer application on spring maize plant height, ear height, fresh weight of stems, brix of stems and stem puncture strength by 2.82%-5.22%, 3.11%-5.90%, 15.96%-19.78%, 4.35%-4.50% and 8.89%-14.82%, respectively. Straw returning increased the effectiveness of potassium fertilizer application on the spring maize grain protein content, spring maize grain crude fat content, maize yield and yield variation coefficient by 3.49%-6.50%, 2.09%-4.43%, 4.87%-12.50% and 5.07%-7.55%, respectively. Straw returning can be combined with reasonable application of potassium fertilizer to increase the effectiveness of potassium fertilizer and enhance lodging resistance. Along with increased maize yield, straw returning also improves grain quality and enhances yield stability, providing a theoretical basis for high-yield and stress-resistant cultivation of Inner Mongolia spring maize, which can be popularized and applied in the spring maize planting areas of Inner Mongolia.
Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data
Authors: Stephens Zachary , O’Brien Daniel , Dehankar Mrunal , Roberts Lewis R. , Iyer Ravishankar K. , Kocher Jean-Pierre 
Published: April 2021

AbstractThe integration of viruses into the human genome is known to be associated with tumorigenesis in many cancers, but the accurate detection of integration breakpoints from short read sequencing data is made difficult by human-viral homologies, viral genome heterogeneity, coverage limitations, and other factors. To address this, we present Exogene, a sensitive and efficient workflow for detecting viral integrations from paired-end next generation sequencing data. Exogene’s read filtering and breakpoint detection strategies yield integration coordinates that are highly concordant with those found in long read validation sets. We demonstrate this concordance across 6 TCGA Hepatocellular carcinoma (HCC) tumor samples, identifying integrations of hepatitis B virus that are validated by long reads. Additionally, we applied Exogene to targeted capture data from 426 previously studied HCC samples, achieving 98.9% concordance with existing methods and identifying 238 high-confidence integrations that were not previously reported. Exogene is applicable to multiple types of paired-end sequence data, including genome, exome, RNA-Seq or targeted capture.
Distribution, prevalence, and causative agents of fungal keratitis: A systematic review and meta-analysis (1990 to 2020)
Authors: Ahmadikia Kazem , Gharehbolagh Sanaz Aghaei , Fallah Bahareh , Naeimi Mahsa , Malekifar Pooneh , Rahsepar Saeedeh , Getso Muhammad Ibrahim , Sharma Savitri , Mahmoudi Shahram 
Published: April 2021

AbstractFungal keratitis is a sight-threatening infection with global distribution. In this systematic review and meta-analysis we collected all the articles with data on the prevalence of fungal keratitis among various patient groups from January 1, 1990 to May 27, 2020. The 169 eligible articles were divided into 6 groups. The pooled prevalence was variable with values ranging from 0.05% among post-keratoplasty patients to 43.01% among patients with a clinical suspicion of fungal keratitis. Except for post-keratoplasty cases (yeast: 51.80%), in all patient groups moulds were more common than yeasts. Although more than 50 distinct species of fungi have been found to cause fungal keratitis,Fusariumspecies followed byAspergillusspecies were the most common causes of the disease. In general, 9.29% (95% CI 6.52, 12.38) of fungal keratitis cases were mixed with bacterial agents.
Neurodevelopment vs. the immune system: complementary contributions of maternally-inherited gene transcripts and proteins to successful egg development in fish
Authors: Żarski Daniel , Cam Aurelie Le , Frohlich Thomas , Kösters Miwako , Klopp Christophe , Nynca Joanna , Ciesielski Sławomir , Sarosiek Beata , Dryl Katarzyna , Montfort Jerome , Król Jarosław , Fontaine Pascal , Ciereszko Andrzej , Bobe Julien 
Published: April 2021

AbstractBackgroundIn Metazoans, embryonic development relies on maternally-inherited mRNAs and proteins that are critical for early developmental success and known to play major roles at later stages, beyond zygotic genome activation. However, very poor concordance between transcript and protein levels in oocytes and embryos of vertebrates suggest that maternally-inherited proteins and maternally-inherited mRNAs are playing different roles in unfertilized eggs, not considered to date comprehensively. The aim of this study was to investigate the respective contribution of maternally-inherited mRNAs and maternally-inherited proteins to egg molecular cargo and to its developmental competence using pikeperch, an ecologically and commercially relevant freshwater fish species, as a model.ResultsOur data shed new light on the importance of maternally-inherited mRNAs in nervous system development suggesting that neurogenesis is a major mRNA-dependent non-genetic inheritance factor. In contrast, our results highlight a specific role of maternally-inherited proteins in immune response in ovulated eggs suggesting that maternal proteins would rather contribute to developmental success through protection of the embryo against pathogens. Further analysis revealed susceptibility of the transcriptome to modifications during the post-vitellogenic processes (i.e., final oocyte maturation and ovulation), whereas proteomic cargo remains unaffected. This may negatively affect developmental competence of the egg and possibly influence further nervous system development of the embryo.ConclusionsOur study provides novel insights into the understanding of type-specific roles of maternally-inherited molecules in fish. Here we show, for the first time, that transcripts and proteins have distinct, yet complementary, functions in the egg of teleost fish. Maternally-inherited mRNAs would shape embryo neurodevelopment and possibly the future behavior of the fish, while maternally-inherited proteins would rather be responsible for protecting the embryo against pathogens. Additionally, we observed that processes directly preceding ovulation may considerably affect the reproductive success by modifying expression level of genes crucial for proper embryonic development, being novel fish egg quality markers (e.g.,smarca4orh3f3a). These results are of major importance for understanding the influence of external factors on reproductive fitness in both captive and wild-type fish species.
Inactivation of SARS-CoV-2 in chlorinated swimming pool water
Authors: Brown Jonathan C , Moshe Maya , Blackwell Alex , Barclay Wendy S 
Published: April 2021

AbstractSARS-CoV-2 transmission remains a global problem which exerts a significant direct cost to public health. Additionally, other aspects of physical and mental health can be affected by limited access to social and exercise venues as a result of lockdowns in the community or personal reluctance due to safety concerns. Swimming pools have reopened in the UK as of April 12th, but the effect of swimming pool water on inactivation of SARS-CoV-2 has not yet been directly demonstrated. Here we demonstrate that water which adheres to UK swimming pool guidelines is sufficient to reduce SARS-CoV-2 infectious titre by at least 3 orders of magnitude.
T cells expressing multiple co-inhibitory molecules in acute malaria are not exhausted but exert a suppressive function
Authors: Brandi Johannes , Lehmann Cari , Kaminski Lea-Christina , zur Wiesch Julian Schulze , Addo Marylyn , Ramharter Michael , Mackroth Maria , Jacobs Thomas , Riehn Mathias 
Published: April 2021

AbstractOverwhelming activation of T cells in acute malaria is associated with severe outcomes. Thus, counter-regulation by anti-inflammatory mechanisms is indispensable for an optimal resolution of disease. UsingPlasmodium bergheiANKA (PbA) infection of C57BL/6 mice, we performed a comprehensive analysis of co-inhibitory molecules expressed on CD4+and CD8+T cells using an unbiased cluster analysis approach. We identified similar T cell clusters co-expressing several co-inhibitory molecules like programmed cell death protein 1 (PD-1) and lymphocyte activation gene 3 (LAG-3) in the CD4+and the CD8+T cell compartment. Interestingly, despite expressing co-inhibitory molecules, which are associated with T cell exhaustion in chronic settings, these T cells were more functional compared to activated T cells that were negative for co-inhibitory molecules. However, T cells expressing high levels of PD-1 and LAG-3 also conferred suppressive capacity and thus resembled type I regulatory T cells. To our knowledge, this is the first description of malaria-induced CD8+T cells with suppressive capacity. Importantly, we found an induction of T cells with a similar co-inhibitory rich phenotype inPlasmodium falciparuminfected patients. In conclusion, we demonstrate that malaria-induced T cells expressing co-inhibitory molecules are not exhausted, but acquire additional suppressive capacity, which might represent an immune regulatory pathway to prevent further activation of T cells during acute malaria.
Endothelial SIRPα signaling controls thymic progenitor homing for T cell regeneration and antitumor immunity
Authors: Ren Boyang , Xia Huan , Liao Yijun , Zhou Hang , Wang Zhongnan , Shi Yaoyao , Zhu Mingzhao 
Published: April 2021

AbstractThymic homing of hematopoietic progenitor cells (HPCs) is an essential step for the subsequent T cell development. Previously we have identified a subset of specialized thymic portal endothelial cells (TPECs), which is important for thymic HPC homing. However, the underlying molecular mechanism remains still unknown. Here we found that signal regulatory protein alpha (SIRPα) is preferentially expressed on TPECs. Disruption of CD47-SIRPα signaling in mice resulted in reduced number of thymic early T cell progenitors (ETPs) and impaired thymic HPC homing. Mechanistically, SIRPα-deficient ECs and CD47-deficient lymphocytes demonstrated impaired transendothelial migration (TEM). Specifically, SIRPα intracellular ITIM motif-initiated downstream signaling in ECs was found to be required for TEM in a SHP2- and Src-dependent manner. Furthermore, CD47-signaling from migrating cells and SIRPα intracellular signaling were found to be required for VE-cadherin endocytosis in ECs. Functionally, SIRPα signaling is required for T cell regeneration upon sub-lethal total body irradiation (SL-TBI); CD47-SIRPα signaling blockade post SL-TBI diminishes antitumor immunity. Thus, our study reveals a novel role of endothelial SIRPα signaling for thymic HPC homing for T cell regeneration and antitumor immunity.Graphic abstractThymic homing of hematopoietic progenitor cells is fundamental to the T cell-based adaptive immunity, yet the molecular basis of this process is less clear. We discovered that endothelial SIRPα signaling, engaged by migrating cell derived CD47 ligand, regulates thymic homing of hematopoietic progenitor cells for T cell regeneration and antitumor immunity.SIRPα is preferentially expressed on thymic portal endothelial cells.Endothelial SIRPα regulates thymic homing of hematopoietic progenitor cells.CD47-SIRPα downstream signaling induces VE-cadherin endocytosis.CD47-SIRPα signaling blockade impairs thymic T cell regeneration and antitumor immunity.
Tire abrasion particles negatively affect plant growth even at low concentrations and alter soil biogeochemical cycling
Authors: Leifheit Eva F , Kissener Hanna L , Faltin Erik , Ryo Masahiro , Rillig Matthias C 
Published: April 2021

AbstractTire particles (TPs) are a major source of microplastic on land, and considering their chemical composition, they represent a potential hazard for the terrestrial environment. We studied the effects of TPs at environmentally relevant concentrations along a wide concentration gradient (0 – 160 mg g−1) and tested the effects on plant growth, soil pH and the key ecosystem process of litter decomposition and soil respiration. The addition of TPs negatively affected shoot and root growth already at low concentrations. Tea litter decomposition slightly increased with lower additions of TPs but decreased later on. Soil pH increased until a TP concentration of 80 mg kg-1 and leveled off afterwards. Soil respiration clearly increased with increasing concentration of added TPs. Plant growth was likely reduced with starting contamination and stopped when contamination reached a certain level in the soil. The presence of TPs altered a number of biogeochemical soil parameters that can have further effects on plant performance. Considering the quantities of yearly produced TPs, their persistence, and toxic potential, we assume that these particles will eventually have a significant impact on terrestrial ecosystems.
“Thinking out loud”: an open-access EEG-based BCI dataset for inner speech recognition
Authors: Nieto Nicolás , Peterson Victoria , Rufiner Hugo Leonardo , Kamienkoski Juan , Spies Ruben 
Published: April 2021

ABSTRACTSurface electroencephalography is a standard and noninvasive way to measure electrical brain activity. Recent advances in artificial intelligence led to significant improvements in the automatic detection of brain patterns, allowing increasingly faster, more reliable and accessible Brain-Computer Interfaces. Different paradigms have been used to enable the human-machine interaction and the last few years have broad a mark increase in the interest for interpreting and characterizing the “inner voice” phenomenon. This paradigm, called inner speech, raises the possibility of executing an order just by thinking about it, allowing a “natural” way of controlling external devices. Unfortunately, the lack of publicly available electroencephalography datasets, restricts the development of new techniques for inner speech recognition. A ten-subjects dataset acquired under this and two others related paradigms, obtained with an acquisition system of 136 channels, is presented. The main purpose of this work is to provide the scientific community with an open-access multiclass electroencephalography database of inner speech commands that could be used for better understanding of the related brain mechanisms.
Alternative splicing of pericentrin contributes to cell cycle control in cardiomyocytes
Authors: Steinfeldt Jakob , Becker Robert , Vergarajauregui Silvia , Engel Felix B. 
Published: April 2021

AbstractInduction of cardiomyocyte proliferation is a promising option to regenerate the heart. Thus, it is important to elucidate mechanisms that contribute to the cell cycle arrest of mammalian cardiomyocytes. Here, we assessed the contribution of the pericentrin (Pcnt) S isoform to the cell cycle arrest in postnatal cardiomyocytes. Immunofluorescence staining of Pcnt isoforms combined with siRNA-mediated depletion indicates that Pcnt S preferentially localizes to the nuclear envelope, while the Pcnt B isoform is enriched at centrosomes. This is further supported by the localization of ectopically expressed FLAG-tagged Pcnt S and Pcnt B in postnatal cardiomyocytes. Analysis of centriole configuration upon Pcnt depletion revealed that Pcnt B but not Pcnt S is required for centriole cohesion. Importantly, ectopic expression of Pcnt S induced centriole splitting in a heterologous system, ARPE-19 cells, and was sufficient to impair DNA synthesis in C2C12 myoblasts. Moreover, Pcnt S depletion enhanced serum-induced cell cycle re-entry in postnatal cardiomyocytes. Analysis of mitosis, binucleation rate, and cell number suggests that Pcnt S depletion promotes progression of postnatal cardiomyocytes through the cell cycle resulting in cell division. Collectively, our data indicate that alternative splicing of Pcnt contributes to the establishment of cardiomyocyte cell cycle arrest shortly after birth.
Let’s Do the Time Warp Again: Non-linear time series matching as a tool for sequentially structured data in ecology
Authors: Hegg Jens C. , Kennedy Brian P. 
Published: April 2021

AbstractEcological patterns are often fundamentally chronological. However, generalization of data is necessarily accompanied by a loss of detail or resolution. Temporal data in particular contains information not only in data values but in the temporal structure, which is lost when these values are aggregated to provide point estimates. Dynamic Time Warping (DTW) is a time series comparison method that is capable of efficiently comparing series despite temporal offsets that confound other methods. The DTW method is both efficient and remarkably flexible, capable of efficiently matching not only time series but any sequentially structured dataset, which has made it a popular technique in machine learning, artificial intelligence, and big data analytical tasks. DTW is rarely used in ecology despite the ubiquity of temporally structured data. As technological advances have increased the richness of small-scale ecological data, DTW may be an attractive analysis technique because it is able to utilize the additional information contained in the temporal structure of many ecological datasets. In this study we use an example dataset of high-resolution fish movement records obtained from otolith microchemistry to compare traditional analysis techniques with DTW clustering. Our results suggest that DTW is capable of detecting subtle behavioral patterns within otolith datasets which traditional data aggregation techniques cannot. These results provide evidence that the DTW method may be useful across many of the temporal data types commonly collected in ecology, as well other sequentially ordered “pseudo time series” data such as classification of species by shape.Keywords:classification, cluster analysis, data generalization, DTW, dynamic time warping, otolith chemistry, time series
Ageing via sexual perception is a by-product of male adaptive plasticity inDrosophila melanogaster
Authors: Corbel Quentin , Serra Manuel , García-Roa Roberto , Carazo Pau 
Published: April 2021

ABSTRACTSensory perception of environmental cues can dramatically modulate ageing across distant taxa. For example, maleDrosophila melanogasterage faster if they perceive female cues but fail to mate (ageing via sexual perception). This finding has been a breakthrough for our understanding of the mechanisms of ageing, yet we ignore how and why such responses have evolved. Here, we usedD. melanogasterto ask whether ageing via sexual perception may be a by-product of plastic adaptive responses to female cues, and found that while long-term sexual perception leads to reproductive costs, short-term perception increases male lifetime reproductive success in a competitive environment. Simulations under a wide range of socio-sexual and demographic scenario suggest that such plasticity as a response to sexual perception might be a widespread strategy in nature. Finally, we show that sexual perception can significantly magnify sexual selection (15-27% average increase in the opportunity for selection).
Herbivory enhances leaky sex expression in the dioecious herbMercurialis annua
Authors: Villamil Nora , Li Xinji , Seddon Emily , Pannell John R. 
Published: April 2021

AbstractPlant reproductive traits are widely understood to be responsive to the selective pressures exerted by pollinators, but there is also increasing evidence for an important role of antagonists such as herbivores in shaping these traits. Many dioecious species show leaky sex expression, with males and females occasionally producing flowers of the opposite sex. Here we show that leaky sex expression in both males and females of the wind-pollinated dioecious herbMercurialis annua(Euphorbiaceae) is enhanced in response to simulated herbivory, increasing the probability and the degree of leakiness in both sexes. We also found that leakiness was greater in larger females but not in larger males. We discuss hypotheses for a possible functional link between herbivory and leaky sex expression, and consider what herbivory-induced leakiness might imply for the evolutionary ecology of plant reproductive systems, especially the breakdown of dioecy and the evolution of hermaphroditism.
Nascent clathrin lattices spontaneously disassemble without sufficient adaptor proteins
Authors: Guo Si-Kao , Sodt Alexander J. , Johnson Margaret E. 
Published: April 2021

AbstractClathrin-coated structures must assemble on cell membranes to perform their primary function of receptor internalization. These structures show marked plasticity and instability, but what conditions are necessary to stabilize against disassembly have not been quantified. Recentin vitrofluorescence experiments have measured kinetics of stable clathrin assembly on membranes as controlled by key adaptor proteins like AP-2. Here, we combine this experimental data with microscopic reaction-diffusion simulations and theory to quantify mechanisms of stable vs unstable clathrin assembly on membranes. Both adaptor binding and dimensional reduction on the 2D surface are necessary to reproduce the cooperative kinetics of assembly. By applying our model to more physiologic-like conditions, where the stoichiometry and volume to area ratio are significantly lower thanin vitro, we show that the critical nucleus contains~25 clathrin, remarkably similar to sizes of abortive structures observedin vivo. Stable nucleation requires a stoichiometry of adaptor to clathrin that exceeds 1:1, meaning that AP-2 on its own has too few copies to nucleate lattices. Increasing adaptor concentration increases lattice sizes and nucleation speeds. For curved clathrin cages, we quantify both the cost of bending the membrane and the stabilization required to nucleate cages in solution. We find the energetics are comparable, suggesting that curving the lattice could offset the bending energy cost. Our model predicts how adaptor density controls stabilization of clathrin-coated structures against spontaneous disassembly, and shows remodeling and disassembly does not require ATPases, which is a critical advance towards predicting control of productive vesicle formation.Significance StatementStochastic self-assembly of clathrin-coated structures on the plasma membrane is essential for transport into cells. We show here that even with abundant clathrin available, robust nucleation and growth into stable structures on membranes is not possible without sufficient adaptor proteins. Our results thus provide quantitative justification for why structures observed to formin vivocan still spontaneously disassemble over many seconds. The ATPases that drive clathrin disassembly after productive vesicle formation are therefore not necessary to control remodeling during growth. With parameterization againstin vitrokinetics of assembly on membranes, our reaction-diffusion model provides a powerful and extensible tool for establishing determinants of productive assembly in cells.