Miracle-dz/UniFAR-FTUs huggingface dataset:
Cotton leafroll dwarf disease: An enigmatic viral disease in cotton

Abstract Taxonomy: Cotton leafroll dwarf virus (CLRDV) is a member of the genus Polerovirus, family Solemoviridae. Geographical Distribution: CLRDV is present in most cotton‐producing regions worldwide, prominently in North and South America. Physical Properties: The virion is a nonenveloped icosahedron with T = 3 icosahedral lattice symmetry that has a diameter of 26–34 nm and comprises 180 molecules of the capsid protein. The CsCl buoyant density of the virion is 1.39–1.42 g/cm3 and S20w is 115–127S. Genome: CLRDV shares genomic features with other poleroviruses; its genome consists of monopartite, single‐stranded, positive‐sense RNA, is approximately 5.7–5.8 kb in length, and is composed of seven open reading frames (ORFs) with an intergenic region between ORF2 and ORF3a. Transmission: CLRDV is transmitted efficiently by the cotton aphid (Aphis gossypii Glover) in a circulative and nonpropagative manner. Host: CLRDV has a limited host range. Cotton is the primary host, and it has also been detected in different weeds in and around commercial cotton fields in Georgia, USA. Symptoms: Cotton plants infected early in the growth stage exhibit reddening or bronzing of foliage, maroon stems and petioles, and drooping. Plants infected in later growth stages exhibit intense green foliage with leaf rugosity, moderate to severe stunting, shortened internodes, and increased boll shedding/abortion, resulting in poor boll retention. These symptoms are variable and are probably influenced by the time of infection, plant growth stage, varieties, soil health, and geographical location. CLRDV is also often detected in symptomless plants. Control: Vector management with the application of chemical insecticides is ineffective. Some host plant varieties grown in South America are resistant, but all varieties grown in the United States are susceptible. Integrated disease management strategies, including weed management and removal of volunteer stalks, could reduce the abundance of virus inoculum in the field.
The Solvability Conditions for one Kind of Matrix Indefinite Problems

In this paper,the matrix indefinite problem min X∈Rn×strC-AXBTJC-AXBhas been discussed.Using Kronecker Products,the vec Operator and the hyperbolic QR factorization of matrices,the necessary and sufficient conditions for problem exist solutions are given,and a general form of the solution set is presented when the problem is solvable.
Third-trimester cervical length assessment for the prediction of spontaneous late preterm birth

Abstract Background The usefulness of cervical length (CL) measurement in asymptomatic pregnancies in the third trimester of pregnancy is not certain. Therefore, the objective of this study was to assess the performance of CL measurement at 31–34 gestational weeks for the prediction of spontaneous late preterm birth (PTB). Materials and Methods This was a prospective study of women with a singleton pregnancy, who had their routine third-trimester scan at 31–34 weeks. The CL was measured transvaginally and was tested, together with maternal demographic and obstetric parameters, for the prediction of late PTB (34 to 36 weeks), using logistic regression and ROC curve analysis. Results Overall, from a population of 1003 women that consented to participate in the study, 42 (4.2%) delivered at 34–36 gestational weeks. A significant association was identified between gestational age at birth and CL (rho = 0.182, p < .001), and there were significant differences in the CL between cases of late preterm and term births (p < .001). Cervical length alone could predict 17% of late PTB for a 10% false positive rate, corresponding to 22 mm. A model combining CL with parity and method of conception can identify 35% of pregnancies resulting in late PTB, at a false positive rate of 10% (AUC: 0.750; 95% CI: 0.675–0.824). Conclusions CL assessment at 31–34 gestational weeks may contribute to the prediction of late PTB when combined with maternal characteristics.
Circumstellar Chemistry and Dust from Dead Stars in Meteorites

This chapter briefly introduces the chemistry in circumstellar envelopes (CSE) around old, mass-losing stars. The focus is on stars with initial masses of one to eight solar masses that evolve into red giant stars with a few hundred times the solar radius, and which develop circumstellar shells several hundred times their stellar radii. The chemistry in the innermost circumstellar shell adjacent to the photosphere is dominated by thermochemistry, whereas photochemistry driven by interstellar UV radiation dominates in the outer shell. The conditions in the CSE allow mineral condensation within a few stellar radii, and these grains are important sources of interstellar dust. Micron-sized dust grains that formed in the CSE of red giant stars have been isolated from certain meteorites and their elemental and isotopic chemistry provides detailed insights into nucleosynthesis processes and dust formation conditions of their parent stars, which died before the solar system was bom 4.56 Ga ago.
SHP-1 localization to the activating immune synapse promotes NK cell tolerance in MHC class I deficiency

Natural killer (NK) cells recognize virally infected cells and tumors. NK cell function depends on balanced signaling from activating receptors, recognizing products from tumors or viruses, and inhibitory receptors (such as KIR/Ly49), which recognize major histocompatibility complex class I (MHC-I) molecules. KIR/Ly49 signaling preserves tolerance to self but also conveys reactivity toward MHC-I–low target cells in a process known as NK cell education. Here, we found that NK cell tolerance and education were determined by the subcellular localization of the tyrosine phosphatase SHP-1. In mice lacking MHC-I molecules, uneducated, self-tolerant Ly49A+ NK cells showed accumulation of SHP-1 in the activating immune synapse, where it colocalized with F-actin and the signaling adaptor protein SLP-76. Education of Ly49A+ NK cells by the MHC-I molecule H2Dd led to reduced synaptic accumulation of SHP-1, accompanied by augmented signaling from activating receptors. Education was also linked to reduced transcription of Ptpn6, which encodes SHP-1. Moreover, synaptic SHP-1 accumulation was reduced in NK cells carrying the H2Dd-educated receptor Ly49G2 but not in those carrying the noneducating receptor Ly49I. Colocalization of Ly49A and SHP-1 outside of the synapse was more frequent in educated compared with uneducated NK cells, suggesting a role for Ly49A in preventing synaptic SHP-1 accumulation in NK cell education. Thus, distinct patterning of SHP-1 in the activating NK cell synapse may determine NK cell tolerance. Description The spatial patterning of the tyrosine phosphatase SHP-1 in mouse NK cells may determine self-tolerance. Location matters for NK cell education Natural killer (NK) cells recognize and kill virally infected cells and tumor cells. NK cell activation depends on the balance in signaling between activating receptors, which recognize stress-induced cellular ligands, and inhibitory receptors, recognizing MHC class I (MHC-I) molecules, markers of self and determinants of tolerance. During NK cell development, inhibitory receptor signaling ensures that NK cells tolerate self and can respond to activating ligands, a process known as education. Schmied et al. compared uneducated and educated mouse NK cells and found that education altered the subcellular localization of the tyrosine phosphatase SHP-1, which normally inhibits NK cell activation. During education, inhibitory receptors sequestered SHP-1, suggesting a model in which SHP-1 is prevented from accumulating at activating immune synapses between NK cells and their targets, thus facilitating target cell killing. These findings suggest that the spatial patterning of SHP-1 in NK cell synapses through education may facilitate self-tolerance. —JFF
Reporting on a Decade of Promoting Software Engineering for Systems-of-Systems and Software Ecosystems

Systems-of-systems (SoS) have become increasingly complex and frequently used in highly distributed, dynamic, and open environments. SoS refer to evolving software systems in which constituent systems (themselves systems in their own right) cooperatively work to fulfill specific, complex missions, facing Software Engineering researchers and practitioners with substantial challenges. Software ecosystems (SECO) have also become an important research topic, addressing social issues along with technical aspects of software development. SoS and SECO are closely related and naturally distributed in development teams. In both fields, distributed resources aim at reducing cost and reaching new Information Technology markets. Software Engineering-related problems and challenges are amplified and become more critical when SoS and SECO are analyzed together. The 10th IEEE/ACM International Workshop on Software Engineering for Systems-of-Systems and Software Ecosystems (SESoS 2022) celebrates a decade of promoting a forum to exchange ideas and experiences, analyze research and development issues, discuss promising solutions, and propose theoretical foundations for the development and evolution of complex software-intensive systems, inspiring visions for the future of Software Engineering for SoS and SECO, as well as paving the way for a more structured community effort. Based on the community feedback, topics of interest should address systems thinking and complexity of those types of systems. As such, the SESoS community is reflecting on how the different dimensions of those types of systems - technological, organizational, and social - should be addressed in research and practice.
A virtual reality study investigating the train illusion

The feeling of self-movement that occurs in the absence of physical motion is often referred to as vection, which is commonly exemplified using the train illusion analogy (TIA). Limited research exists on whether the TIA accurately exemplifies the experience of vection in virtual environments (VEs). Few studies complemented their vection research with participants' qualitative feedback or by recording physiological responses, and most studies used stimuli that contextually differed from the TIA. We investigated whether vection is experienced differently in a VE replicating the TIA compared to a VE depicting optic flow by recording subjective and physiological responses. Additionally, we explored participants' experience through an open question survey. We expected the TIA environment to induce enhanced vection compared to the optic flow environment. Twenty-nine participants were visually and audibly immersed in VEs that either depicted optic flow or replicated the TIA. Results showed optic flow elicited more compelling vection than the TIA environment and no consistent physiological correlates to vection were identified. The post-experiment survey revealed discrepancies between participants' quantitative and qualitative feedback. Although the dynamic content may outweigh the ecological relevance of the stimuli, it was concluded that more qualitative research is needed to understand participants' vection experience in VEs.
Mortality of Lasioderma serricorne in a Continuously Heated Environment

Abstract. Heat treatment is a potential alternative to chemicals for controlling stored-product insect pests. During heat treatment, attaining uniform temperature across a facility is not possible because of differential heating rates. Effects of different heating rates of 0 (check), 0.5, 5, and 10°C per hour on life stages of Lasioderma serricorne were studied in a laboratory. Different heating rates killed significantly different numbers of L. serricorne life stages, with more killed with increasing exposure at 50°C. Compared to the check, significantly more L. serricorne larvae exposed to continuous heating of 28 to 50°C at 5 and 10°C per hour were killed after exposure at 50°C for 15, 30, 45, and 60 minutes. However, L. serricorne larvae and eggs exposed to continuous heating of 28 to 50°C at 0.5more at different heating ra per hour significantly increased after exposure at 50°C for 15, 30, 45, and 60 minutes. Maintaining temperature at ≥50°C for >90 minutes in a facility killed almost all life stages of L. serricorne. Pupae were least susceptible to heat.
Effects of Host and Parasitoid Ages on Parasitism Efficiency of Dirhinus giffardii (Silvestri) against Zeugodacus cucurbitae

Abstract. Pesticides threaten the environment and increase amounts of resistance by pests. Ecologically friendly biological control of pests is being considered in scientific and political spheres. Fruit flies cause huge economic losses to more than 81 fruit and vegetable species. They are major pests in tropical and subtropical areas. This study used pupae of melon fly, Zeugodacus cucurbitae (Coquillett), as a host and Dirhinus giffardii (Silvestri) as the parasitoid, the biological control agent. During host-parasitoid interaction at different conditions of exposure, the rate of parasitism of a host by D. giffardii differed significantly in time. Least parasitism was of 1-day-old pupae (13.41 ± 1.10) exposed for 6 hours. Greatest percentage of parasitism was to 3-day-old pupae (43.5 ± 1.12) exposed for 24 hours. Few pupae younger than 3 days old were parasitized. Parasitoid emergence rate from pupae increased from 6 hours (21.49 ± 1.46), to 12 hours (28.30 ± 2.00), and 24 hours (33.93 ± 0.66). Percentage of emergence of 3-day-old pupae was 28.40 ± 0.59 at 6 hours, 29.51 ± 0.45 at 12 hours, and 34.11 ± 0.224 at 24 hours. To maximize in vivo production of parasitoids, 5-day-old female D. giffardii should be provided pupae ≤3 days old. Results contribute to further understanding host-parasitoid interaction important for sustainable and integrated pest management practices throughout the world.
A modular metagenomics analysis system for integrated multi-step data exploration

Motivation Computational analysis of large-scale metagenomics sequencing datasets has proved to be both incredibly valuable for extracting isolate-level taxonomic and functional insights from complex microbial communities. However, thanks to an ever-expanding ecosystem of metagenomics-specific algorithms and file formats, designing studies, implementing seamless and scalable end-to-end workflows, and exploring the massive amounts of output data have become studies unto themselves. Furthermore, there is little inter-communication between output data of different analytic purposes, such as short-read classification and metagenome assembled genomes (MAG) reconstruction. One-click pipelines have helped to organize these tools into targeted workflows, but they suffer from general compatibility and maintainability issues. Results To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed a module-based metagenomics analysis system written in Snakemake, a popular workflow management system, along with a standardized module and working directory architecture. Each module can be run independently or conjointly with a series of others to produce the target data format (ex. short-read preprocessing alone, or short-read preprocessing followed by de novo assembly), and outputs aggregated summary statistics reports and semi-guided Jupyter notebook-based visualizations, The module system is a bioinformatics-optimzied scaffold designed to be rapidly iterated upon by the research community at large. Availability The module template as well as the modules described below can be found at https://github.com/MetaSUB-CAMP. Contact lam4003@med.cornell. edu, btt4001@med.cornell. edu, chm2042@med.cornell. edu, or imh2003@med.cornell. edu Supplementary information Supplementary data are available at Bioinformatics online.
Broad functional profiling of fission yeast proteins using phenomics and machine learning

Many proteins remain poorly characterized even in well-studied organisms, presenting a bottleneck for research. We applied phenomics and machine-learning approaches with Schizosaccharomyces pombe for broad cues on protein functions. We assayed colony-growth phenotypes to measure the fitness of deletion mutants for 3509 non-essential genes in 131 conditions with different nutrients, drugs, and stresses. These analyses exposed phenotypes for 3492 mutants, including 124 mutants of ‘priority unstudied’ proteins conserved in humans, providing varied functional clues. For example, over 900 proteins were newly implicated in the resistance to oxidative stress. Phenotype-correlation networks suggested roles for poorly characterized proteins through ‘guilt by association’ with known proteins. For complementary functional insights, we predicted Gene Ontology (GO) terms using machine learning methods exploiting protein-network and protein-homology data (NET-FF). We obtained 56,594 high-scoring GO predictions, of which 22,060 also featured high information content. Our phenotype-correlation data and NET-FF predictions showed a strong concordance with existing PomBase GO annotations and protein networks, with integrated analyses revealing 1,675 novel GO predictions for 783 genes, including 47 predictions for 23 priority unstudied proteins. Experimental validation identified new proteins involved in cellular ageing, showing that these predictions and phenomics data provide a rich resource to uncover new protein functions.
Emergence and rapid dissemination of highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b in wild birds, Chile

In December 2022, HPAI H5N1 clade 2.3. 4.4b emerged in Chile. We detected the virus in 93 wild bird samples and sequenced the whole genome of nine Chilean strains from pelicans and gulls. Phylogenetic analysis suggests at least two different HPAI viral clusters in South America.
Dynamic spatial coding in parietal cortex mediates tactile-motor transformation

Movements towards touch on the body require integrating tactile location and body posture information. Tactile processing and movement planning both rely on posterior parietal cortex (PPC) but their interplay is not understood. Here, human participants received tactile stimuli on their crossed and uncrossed feet, dissociating stimulus location relative to anatomy versus external space. Participants pointed to the touch or the equivalent location on the other foot, which dissociates sensory and motor locations. Multi-voxel pattern analysis of concurrently recorded fMRI signals revealed that tactile location was coded anatomically in anterior PPC but spatially in posterior PPC during sensory processing. After movement instructions were specified, PPC exclusively represented the movement goal in space, in regions associated with visuo-motor planning and with regional overlap for sensory, rule-related, and movement coding. Thus, PPC flexibly updates its spatial codes to accommodate rule-based transformation of sensory input to generate movement to environment and own body alike.
Relaxed Eddy Accumulation Outperforms Monin‐Obukhov Flux Models Under Non‐Ideal Conditions

The Monin‐Obukhov Similarity Theory (MOST) links turbulent statistics to surface fluxes through universal functions. Here, we investigate its performance over a large lake, where none of its assumptions (flat homogeneous surface) are obviously violated. We probe the connection between the variance budget terms and departure from the nondimensional flux‐variance function for CO2, water vapor, and temperature. Our results indicate that both the variance storage and its vertical transport affect MOST, and these terms are most significant when small fluxes and near neutral conditions were prevalent. Such conditions are common over lakes and oceans, especially for CO2, underlining the limitation of using any MOST‐based methods to compute small fluxes. We further show that the relaxed eddy accumulation (REA) method is more robust and less sensitive to storage and transport, adequately reproducing the eddy‐covariance fluxes even for the smallest flux magnitudes. Therefore, we recommend REA over MOST methods for trace‐gas flux estimation.
Toward accurate cerebral blood flow estimation in mice after accounting for anesthesia

Purpose: To improve the accuracy of cerebral blood flow (CBF) measurement in mice by accounting for the anesthesia effects. Methods: The dependence of CBF on anesthesia dose and time was investigated by simultaneously measuring respiration rate (RR) and heart rate (HR) under four different anesthetic regimens. Quantitative CBF was measured by a phase-contrast (PC) MRI technique. RR was evaluated with a mouse monitoring system (MouseOX) while HR was determined using an ultrashort-TE MRI sequence. CBF, RR, and HR were recorded dynamically with a temporal resolution of 1 min in a total of 19 mice. Linear regression models were used to investigate the relationships among CBF, anesthesia dose, RR, and HR. Results: CBF, RR, and HR all showed a significant dependence on anesthesia dose (p < 0.0001). However, the dose in itself was insufficient to account for the variations in physiological parameters, in that they showed a time-dependent change even for a constant dose. RR and HR together can explain 52.6% of the variations in CBF measurements, which is greater than the amount of variance explained by anesthesia dose (32.4%). Based on the multi-parametric regression results, a model was proposed to correct the anesthesia effects in mouse CBF measurements, specifically C B F c o r r e c t e d = C B F + 0.58 R R − 0.41 H R − 32.66 D o s e . We also reported awake-state CBF in mice to be 142.0 ± 8.8 mL/100 g/min, which is consistent with the model-predicted value. Conclusion: The accuracy of CBF measurement in mice can be improved by using a correction model that accounts for respiration rate, heart rate, and anesthesia dose.
The microbial origin of marine autochthonous fluorescent dissolved organic matter

COPYRIGHT © 2023 Zhao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. The microbial origin of marine autochthonous fluorescent dissolved organic matter