bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell transcriptome profiling of buffelgrass (Cenchrus ciliaris) eggs unveils apomictic parthenogenesis signatures
Authors: Ke Yuji , Podio Maricel , Conner Joann , Ozias-Akins Peggy 
Published: May 2021

AbstractApomixis, a type of asexual reproduction in angiosperms, results in progenies that are genetically identical to the mother plant. It is a highly desirable trait in agriculture due to its potential to preserve heterosis of F1 hybrids through subsequent generations. However, no major crops are apomictic. Deciphering mechanisms underlying apomixis becomes one of the alternatives to engineer self-reproducing capability into major crops. Parthenogenesis, a major component of apomixis, commonly described as the ability to initiate embryo formation from the egg cell without fertilization, also can be valuable in plant breeding for doubled haploid production. A deeper understanding of transcriptional differences between parthenogenetic and sexual or non-parthenogenetic eggs can assist with pathway engineering. By conducting laser capture microdissection-based RNA-seq on sexual and parthenogenetic egg cells on the day of anthesis, a de novo transcriptome for the Cenchrus ciliaris egg cells was created, transcriptional profiles that distinguish the parthenogenetic egg from its sexual counterpart were identified, and functional roles for a few transcription factors in promoting natural parthenogenesis were suggested. These transcriptome data expand upon previous gene expression studies and will be a resource for future research on the transcriptome of egg cells in parthenogenetic and sexual genotypes.
An enhanced dual IDW method for high-quality geospatial interpolation
Authors: Li Zhanglin 
Published: May 2021

AbstractMany geoscience problems involve predicting attributes of interest at un-sampled locations. Inverse distance weighting (IDW) is a standard solution to such problems. However, IDW is generally not able to produce favorable results in the presence of clustered data, which is commonly used in the geospatial data process. To address this concern, this paper presents a novel interpolation approach (DIDW) that integrates data-to-data correlation with the conventional IDW and reformulates it within the geostatistical framework considering locally varying exponents. Traditional IDW, DIDW, and ordinary kriging are employed to evaluate the interpolation performance of the proposed method. This evaluation is based on a case study using the public Walker Lake dataset, and the associated interpolations are performed in various contexts, such as different sample data sizes and variogram parameters. The results demonstrate that DIDW with locally varying exponents stably produces more accurate and reliable estimates than the conventional IDW and DIDW. Besides, it yields more robust estimates than ordinary kriging in the face of varying variogram parameters. Thus, the proposed method can be applied as a preferred spatial interpolation method for most applications regarding its stability and accuracy.
Elevated serum SDMA and ADMA at hospital admission predict in-hospital mortality of COVID-19 patients
Authors: Hannemann Juliane , Balfanz Paul , Schwedhelm Edzard , Hartmann Bojan , Ule Johanna , Müller-Wieland Dirk , Dahl Edgar , Dreher Michael , Marx Nikolaus , Böger Rainer 
Published: May 2021

AbstractCOVID-19 is a disease with a variable clinical course ranging from mild symptoms to critical illness, organ failure, and death. Prospective biomarkers may help to predict the severity of an individual’s clinical course and mortality risk. We analyzed asymmetric (ADMA) and symmetric dimethylarginine (SDMA) in blood samples from 31 patients hospitalized for COVID-19. We calculated associations of ADMA and SDMA with mortality and organ failure, and we developed a predictive algorithm based upon these biomarkers to predict mortality risk. Nine patients (29%) experienced in-hospital death. SDMA and ADMA serum concentrations were significantly higher at admission in COVID-19 patients who died than in survivors. Cut-offs of 0.90 µmol/L for SDMA (AUC, 0.904, p = 0.0005) and 0.66 µmol/L for ADMA (AUC, 0.874, p = 0.0013) were found in ROC analyses to best discriminate both subgroups of patients. Hazard ratio for in-hospital mortality was 12.2 (95% CI: 2.2–31.2) for SDMA and 6.3 (1.1–14.7) for ADMA above cut-off. Sequential analysis of both biomarkers allowed discriminating a high-risk group (87.5% mortality) from an intermediate-risk group (25% mortality) and a low-risk group (0% mortality). Elevated circulating concentrations of SDMA and ADMA may help to better identify COVID-19 patients with a high risk of in-hospital mortality.
Cage and maternal effects on the bacterial communities of the murine gut
Authors: Singh Gurdeep , Brass Andrew , Cruickshank Sheena M. , Knight Christopher G. 
Published: May 2021

AbstractFindings from gut microbiome studies are strongly influenced by both experimental and analytical factors that can unintentionally bias their interpretation. Environment is also critical. Both co-housing and maternal effects are expected to affect microbiomes and have the potential to confound other manipulated factors, such as genetics. We therefore analysed microbiome data from a mouse experiment using littermate controls and tested differences among genotypes (wildtype versus colitis prone-mdr1a−/−), gut niches (stool versus mucus), host ages (6 versus 18 weeks), social groups (co-housed siblings of different genotypes) and maternal influence. We constructed a 16S phylogenetic tree from bacterial communities, fitting random forest models using all 428,234 clades identified. Models discriminated all criteria except host genotype, where no community differences were found. Host social groups differed in abundant, low-level, taxa whereas intermediate phylogenetic and abundance scales distinguished ages and niches. Thus, a carefully controlled experiment treating evolutionary clades of microbes equivalently without reference to taxonomy, clearly identifies whether and how gut microbial communities are distinct across ecologically important factors (niche and host age) and other experimental factors, notably cage effects and maternal influence. These findings highlight the importance of considering such environmental factors in future microbiome studies.
Methylmercury induces neuronal cell death by inducing TNF-α expression through the ASK1/p38 signaling pathway in microglia
Authors: Toyama Takashi , Hoshi Takayuki , Noguchi Takuya , Saito Yoshiro , Matsuzawa Atsushi , Naganuma Akira , Hwang Gi-Wook 
Published: May 2021

AbstractWe recently found that tumor necrosis factor-α (TNF-α) may be involved in neuronal cell death induced by methylmercury in the mouse brain. Here, we examined the cells involved in the induction of TNF-α expression by methylmercury in the mouse brain by in situ hybridization. TNF-α-expressing cells were found throughout the brain and were identified as microglia by immunostaining for ionized calcium binding adaptor molecule 1 (Iba1). Methylmercury induced TNF-α expression in mouse primary microglia and mouse microglial cell line BV2. Knockdown of apoptosis signal-regulating kinase 1 (ASK1), an inflammatory cytokine up-regulator that is responsible for reactive oxygen species (ROS), decreased methylmercury-induced TNF-α expression through decreased phosphorylation of p38 MAP kinase in BV2 cells. Suppression of methylmercury-induced reactive oxygen species (ROS) by antioxidant treatment largely abolished the induction of TNF-α expression and phosphorylation of p38 by methylmercury in BV2 cells. Finally, in mouse brain slices, the TNF-α antagonist (WP9QY) inhibited neuronal cell death induced by methylmercury, as did the p38 inhibitor SB203580 and liposomal clodronate (a microglia-depleting agent). These results indicate that methylmercury induces mitochondrial ROS that are involved in activation of the ASK1/p38 pathway in microglia and that this is associated with induction of TNF-α expression and neuronal cell death.
10-hydroxy-2E-decenoic acid (10HDA) does not promote caste differentiation in Melipona scutellaris stingless bees
Authors: Borges Luiza Diniz Ferreira , Batista Letícia Leandro , Malta Serena Mares , Rodrigues Tamiris Sabrina , Silva Jéssica Regina da Costa , Venturini Gabriela , Pereira Alexandre da Costa , Guedes Pedro Henrique Gonçalves , Ueira-Vieira Carlos , Bonetti Ana Maria 
Published: May 2021

AbstractIn bees from genusMelipona, differential feeding is not enough to fully explain female polyphenism. In these bees, there is a hypothesis that in addition to the environmental component (food), a genetic component is also involved in caste differentiation. This mechanism has not yet been fully elucidated and may involve epigenetic and metabolic regulation. Here, we verified that the genes encoding histone deacetylases HDAC1 and HDAC4 and histone acetyltransferase KAT2A were expressed at all stages ofMelipona scutellaris, with fluctuations between developmental stages and castes. In larvae, the HDAC genes showed the same profile of Juvenile Hormone titers—previous reported—whereas the HAT gene exhibited the opposite profile. We also investigated the larvae and larval food metabolomes, but we did not identify the putative queen-fate inducing compounds, geraniol and 10-hydroxy-2E-decenoic acid (10HDA). Finally, we demonstrated that the histone deacetylase inhibitor 10HDA—the major lipid component of royal jelly and hence a putative regulator of honeybee caste differentiation—was unable to promote differentiation in queens inMelipona scutellaris. Our results suggest that epigenetic and hormonal regulations may act synergistically to drive caste differentiation inMeliponaand that 10HDA is not a caste-differentiation factor inMelipona scutellaris.
Improving radiologist's ability in identifying particular abnormal lesions on mammograms through training test set with immediate feedback
Authors: Trieu Phuong Dung , Lewis Sarah J. , Li Tong , Ho Karen , Wong Dennis J. , Tran Oanh T. M. , Puslednik Louise , Black Deborah , Brennan Patrick C. 
Published: May 2021

AbstractIt has been shown that there are differences in diagnostic accuracy of cancer detection on mammograms, from below 50% in developing countries to over 80% in developed world. One previous study reported that radiologists from a population in Asia displayed a low mammographic cancer detection of 48% compared with over 80% in developed countries, and more importantly, that most lesions missed by these radiologists were spiculated masses or stellate lesions. The aim of this study was to explore the performance of radiologists after undertaking a training test set which had been designed to improve the capability in detecting a specific type of cancers on mammograms. Twenty-five radiologists read two sets of 60 mammograms in a standardized mammogram reading room. The first test set focused on stellate or spiculated masses. When radiologists completed the first set, the system displayed immediate feedback to the readers comparing their performances in each case with the truth of cancer cases and cancer types so that the readers could identify individual-based errors. Later radiologists were asked to read the second set of mammograms which contained different types of cancers including stellate/spiculated masses, asymmetric density, calcification, discrete mass and architectural distortion. Case sensitivity, lesion sensitivity, specificity, receiver operating characteristics (ROC) and Jackknife alternative free-response receiver operating characteristics (JAFROC) were calculated for each participant and their diagnostic accuracy was compared between two sessions. Results showed significant improvement among radiologists in case sensitivity (+ 11.4%; P < 0.05), lesion sensitivity (+ 18.7%; P < 0.01) and JAFROC (+ 11%; P < 0.01) in the second set compared with the first set. The increase in diagnostic accuracy was also recorded in the detection of stellate/spiculated mass (+ 20.6%; P < 0.05). This indicated that the performance of radiologists in detecting malignant lesions on mammograms can be improved if an appropriate training intervention is applied after the readers’ weakness and strength are identified.
African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors associated with immunologic functions and environmental exposures
Authors: Singh Urminder , Hernandez Kyle M. , Aronow Bruce J. , Wurtele Eve Syrkin 
Published: May 2021

AbstractThe COVID-19 pandemic has affected African American populations disproportionately with respect to prevalence, and mortality. Expression profiles represent snapshots of combined genetic, socio-environmental (including socioeconomic and environmental factors), and physiological effects on the molecular phenotype. As such, they have potential to improve biological understanding of differences among populations, and provide therapeutic biomarkers and environmental mitigation strategies. Here, we undertook a large-scale assessment of patterns of gene expression between African Americans and European Americans, mining RNA-Seq data from 25 non-diseased and diseased (tumor) tissue-types. We observed the widespread enrichment of pathways implicated in COVID-19 and integral to inflammation and reactive oxygen stress. Chemokine CCL3L3 expression is up-regulated in African Americans. GSTM1, encoding a glutathione S-transferase that metabolizes reactive oxygen species and xenobiotics, is upregulated. The little-studied F8A2 gene is up to 40-fold more highly expressed in African Americans; F8A2 encodes HAP40 protein, which mediates endosome movement, potentially altering the cellular response to SARS-CoV-2. African American expression signatures, superimposed on single cell-RNA reference data, reveal increased number or activity of esophageal glandular cells and lung ACE2-positive basal keratinocytes. Our findings establishbasal prognostic signaturesthat can be used to refine approaches to minimize risk of severe infection and improve precision treatment of COVID-19 for African Americans. To enable dissection ofcausesof divergent molecular phenotypes, we advocate routine inclusion of metadata on genomic and socio-environmental factors for human RNA-sequencing studies.
A TILLING by sequencing approach to identify induced mutations in sunflower genes
Authors: Fanelli Valentina , Ngo Kathie J. , Thompson Veronica L. , Silva Brennan R. , Tsai Helen , Sabetta Wilma , Montemurro Cinzia , Comai Luca , Harmer Stacey L. 
Published: May 2021

AbstractThe Targeting Induced Local Lesions in Genomes (TILLING) technology is a reverse genetic strategy broadly applicable to every kind of genome and represents an attractive tool for functional genomic and agronomic applications. It consists of chemical random mutagenesis followed by high-throughput screening of point mutations in targeted genomic regions. Although multiple methods for mutation discovery in amplicons have been described, next-generation sequencing (NGS) is the tool of choice for mutation detection because it quickly allows for the analysis of a large number of amplicons. The aim of the present work was to screen a previously generated sunflower TILLING population and identify alterations in genes involved in several important and complex physiological processes. Twenty-one candidate sunflower genes were chosen as targets for the screening. The TILLING by sequencing strategy allowed us to identify multiple mutations in selected genes and we subsequently validated 16 mutations in 11 different genes through Sanger sequencing. In addition to addressing challenges posed by outcrossing, our detection and validation of mutations in multiple regulatory loci highlights the importance of this sunflower population as a genetic resource.
Development and characterization of two equine formulations towards SARS-CoV-2 proteins for the potential treatment of COVID-19
Authors: León Guillermo , Herrera María , Vargas Mariángela , Arguedas Mauricio , Sánchez Andrés , Segura Álvaro , Gómez Aarón , Solano Gabriela , Corrales-Aguilar Eugenia , Risner Kenneth , Narayanan Aarthi , Bailey Charles , Villalta Mauren , Hernández Andrés , Sánchez Adriana , Cordero Daniel , Solano Daniela , Durán Gina , Segura Eduardo , Cerdas Maykel , Umaña Deibid , Moscoso Edwin , Estrada Ricardo , Gutiérrez Jairo , Méndez Marcos , Castillo Ana Cecilia , Sánchez Laura , Sánchez Ronald , Gutiérrez José María , Díaz Cecilia , Alape Alberto 
Published: May 2021

AbstractIn the current global emergency due to SARS-CoV-2 outbreak, passive immunotherapy emerges as a promising treatment for COVID-19. Among animal-derived products, equine formulations are still the cornerstone therapy for treating envenomations due to animal bites and stings. Therefore, drawing upon decades of experience in manufacturing snake antivenom, we developed and preclinically evaluated two anti-SARS-CoV-2 polyclonal equine formulations as potential alternative therapy for COVID-19. We immunized two groups of horses with either S1 (anti-S1) or a mixture of S1, N, and SEM mosaic (anti-Mix) viral recombinant proteins. Horses reached a maximum anti-viral antibody level at 7 weeks following priming, and showed no major adverse acute or chronic clinical alterations. Two whole-IgG formulations were prepared via hyperimmune plasma precipitation with caprylic acid and then formulated for parenteral use. Both preparations had similar physicochemical and microbiological quality and showed ELISA immunoreactivity towards S1 protein and the receptor binding domain (RBD). The anti-Mix formulation also presented immunoreactivity against N protein. Due to high anti-S1 and anti-RBD antibody content, final products exhibited high in vitro neutralizing capacity of SARS-CoV-2 infection, 80 times higher than a pool of human convalescent plasma. Pre-clinical quality profiles were similar among both products, but clinical efficacy and safety must be tested in clinical trials. The technological strategy we describe here can be adapted by other producers, particularly in low- and middle-income countries.
Differential effects of alkaloids on memory in rodents
Authors: Callahan Patrick M. , Terry Alvin V. , Peitsch Manuel C. , Hoeng Julia , Koshibu Kyoko 
Published: May 2021

AbstractNicotinic acetylcholine receptors (nAChRs) play a critical role in the neuropharmacology of learning and memory. As such, naturally occurring alkaloids that regulate nAChR activity have gained interest for understanding and potentially improving memory function. In this study, we tested the acute effects of three known nicotinic alkaloids, nicotine, cotinine, and anatabine, in suppressing scopolamine-induced memory deficit in rodents by using two classic memory paradigms, Y-maze and novel object recognition (NOR) in mice and rats, respectively. We found that all compounds were able to suppress scopolamine-induced spatial memory deficit in the Y-maze spontaneous alternation paradigm. However, only nicotine was able to suppress the short-term object memory deficit in NOR, despite the higher doses of cotinine and anatabine used to account for their potential differences in nAChR activity. These results indicate that cotinine and anatabine can uniquely regulate short-term spatial memory, while nicotine seems to have more robust and general role in memory regulation in rodents. Thus, nAChR-activating alkaloids may possess distinct procognitive properties in rodents, depending on the memory types examined.
Evaluation of grain boundaries as percolation pathways in quartz-rich continental crust using Atomic Force Microscopy
Authors: Dobe Ritabrata , Das Anuja , Mukherjee Rabibrata , Gupta Saibal 
Published: May 2021

AbstractHydrous fluids play a vital role in the chemical and rheological evolution of ductile, quartz-bearing continental crust, where fluid percolation pathways are controlled by grain boundary domains. In this study, widths of grain boundary domains in seven quartzite samples metamorphosed under varying crustal conditions were investigated using Atomic Force Microscopy (AFM) which allows comparatively easy, high magnification imaging and precise width measurements. It is observed that dynamic recrystallization at higher metamorphic grades is much more efficient at reducing grain boundary widths than at lower temperature conditions. The concept of force-distance spectroscopy, applied to geological samples for the first time, allows qualitative estimation of variations in the strength of grain boundary domains. The strength of grain boundary domains is inferred to be higher in the high grade quartzites, which is supported by Kernel Average Misorientation (KAM) studies using Electron Backscatter Diffraction (EBSD). The results of the study show that quartzites deformed and metamorphosed at higher grades have narrower channels without pores and an abundance of periodically arranged bridges oriented at right angles to the length of the boundary. We conclude that grain boundary domains in quartz-rich rocks are more resistant to fluid percolation in the granulite rather than the greenschist facies.
Laser-induced thermal grating spectroscopy based on femtosecond laser multi-photon absorption
Authors: Ruchkina Maria , Hot Dina , Ding Pengji , Hosseinnia Ali , Bengtsson Per-Erik , Li Zhongshan , Bood Joakim , Sahlberg Anna-Lena 
Published: May 2021

AbstractLaser-induced grating spectroscopy (LIGS) is for the first time explored in a configuration based on the crossing of two focused femtosecond (fs) laser pulses (800-nm wavelength) and a focused continuous-wave (cw) laser beam (532-nm wavelength). A thermal grating was formed by multi-photon absorption of the fs-laser pulses by $$\hbox {N}_{{2}}$$

N
2

with a pulse energy around 700 $$\upmu $$
μ
J ($$\sim $$
∼
45 TW/$$\hbox {cm}^{2}$$

cm
2

). The feasibility of this LIGS configuration was investigated for thermometry in heated nitrogen gas flows. The temperature was varied from room temperature up to 750 K, producing strong single-shot LIGS signals. A model based on the solution of the linearized hydrodynamic equations was used to extract temperature information from single-shot experimental data, and the results show excellent agreement with the thermocouple measurements. Furthermore, the fluorescence produced by the fs-laser pulses was investigated. This study indicates an 8-photon absorption pathway for $$\hbox {N}_{{2}}$$

N
2

in order to reach the $$\hbox {B}^{3}\Pi _{g}$$

B
3

Π
g

state from the ground state, and 8 + 5 photon excitation to reach the $$\hbox {B}^{2}\Sigma _{u}^{+}$$

B
2

Σ

u

+

state of the $$\hbox {N}_{2}^{+}$$

N

2

+

ion. At pulse energies higher than 1 mJ, the LIGS signal was disturbed due to the generation of plasma. Additionally, measurements in argon gas and air were performed, where the LIGS signal for argon shows lower intensity compared to air and $$\hbox {N}_{{2}}$$

N
2

.