Miracle-dz/UniFAR-FTUs huggingface dataset:
Astronomical context of Solar System formation from molybdenum isotopes in meteorite inclusions

Timing Solar System formation The oldest solids that formed in the Solar System are calcium-aluminium–rich inclusions (CAIs), small metallic droplets that were later incorporated into meteorites. The ages of CAIs are conventionally taken as the age of the Solar System, but which exact moment in star formation they correspond to has been unclear. Brennecka et al. measured molybdenum isotope ratios in CAIs and found a wide range of origins in both the inner and outer Solar System. They propose that CAIs formed from heterogeneous material accreting from the presolar nebula and that the ages of CAIs coincide with the Sun's transition from a protostar to a pre–main sequence star. Science, this issue p. 837 Molybdenum isotopes in calcium-aluminum–rich inclusions constrain the early history of the Solar System. Calcium-aluminum–rich inclusions (CAIs) in meteorites are the first solids to have formed in the Solar System, defining the epoch of its birth on an absolute time scale. This provides a link between astronomical observations of star formation and cosmochemical studies of Solar System formation. We show that the distinct molybdenum isotopic compositions of CAIs cover almost the entire compositional range of material that formed in the protoplanetary disk. We propose that CAIs formed while the Sun was in transition from the protostellar to pre–main sequence (T Tauri) phase of star formation, placing Solar System formation within an astronomical context. Our results imply that the bulk of the material that formed the Sun and Solar System accreted within the CAI-forming epoch, which lasted less than 200,000 years.
Fertility Behavior and Depression Among Women: Evidence From China

Using data from the China Labor-Force Dynamic Survey, this study employed logistic regressions to investigate the association between fertility behavior and depression among Chinese women. The empirical results show that in China, women having children were significantly less likely to have depressive symptoms (OR = 0.651) compared to childless women. We also found a U-shaped relationship between fertility levels and depression in women. The results were robust to using the propensity score matching approach to address the sample selection problem. Further, our heterogeneity analysis demonstrated that the negative relationship between fertility level and depression was more significant among women who were in their 30s, lived in urban areas, and lived in high-income households. Compared to having male children (boys) (OR = 0.874), having female children (girls) (OR = 0.795) was more significantly associated with fewer depressive symptoms among women. In the meantime, we did not find a significant relationship between the childbearing period and depression. The paper discussed possible reasons for our findings and policy implications from the perspectives of the government, society, and family.
Biostimulant Effects of Glutacetine® and Its Derived Formulations Mixed With N Fertilizer on Post-heading N Uptake and Remobilization, Seed Yield, and Grain Quality in Winter Wheat

Biostimulants could play an important role in agriculture particularly for increasing N fertilizer use efficiency that is essential for maintaining both yield and grain quality in bread wheat, which is a major global crop. In the present study, we examined the effects of mixing urea–ammonium–nitrate fertilizer (UAN) or urea with five new biostimulants containing Glutacetine® or its derivative formulations (VNT1, 2, 3, and 4) on the physiological responses, agronomic traits, and grain quality of winter wheat. A first experiment under greenhouse conditions showed that VNT1, VNT3, and VNT4 significantly increased the seed yield and grain numbers per ear. VNT4 also enhanced total plant nitrogen (N) and total grain N, which induced a higher N Harvest Index (NHI). The higher post-heading N uptake (for VNT1 and VNT4) and the acceleration of senescence speed with all formulations enabled better nutrient remobilization efficiency, especially in terms of N mobilization from roots and straw toward the grain with VNT4. The grain ionome was changed by the formulations with the bioavailability of iron improved with the addition of VNT4, and the phytate concentrations in flour were reduced by VNT1 and VNT4. A second experiment in three contrasting field trials confirmed that VNT4 increased seed yield and N use efficiency. Our investigation reveals the important role of these new formulations in achieving significant increases in seed yield and grain quality.
Therapy Dogs' and Handlers' Behavior and Salivary Cortisol During Initial Visits in a Complex Medical Institution: A Pilot Study

Therapy dogs provide health benefits for individuals who suffer from illnesses, such as dementia, depression, loneliness, and aggression. Therapy dogs' impact on human health has been thoroughly studied; however, studies on dog welfare have been limited. Additionally, as dogs have evolved with humans, they have learned to read non-verbal social cues. Dogs can read humans' non-verbal body language and can react to their emotions. However, the body language of dogs is poorly understood and can lead to dog owner-directed aggression. Communication plays a vital role to be a cohesive therapy team. The purpose of this study was to assess perceived stress and cortisol concentrations in therapy dogs and their handlers during the first three visits in a hospital setting. Moreover, the study aimed to investigate whether, while in an overstimulating environment, a therapy dog handler can observe his or her dog's body language and correlate such observations to the dog's stress. Nine therapy dog teams from Mayo Clinic's Caring Canine Program participated in this study. A baseline salivary cortisol was collected from the handler and therapy dog each day of the visits. Once the team arrived, a pre-visit salivary cortisol was collected from the handler and therapy dog and, afterward, a post-visit salivary cortisol. Handlers were also asked to fill out a perceived stress survey on their own stress and that of their therapy dogs'. Behavior was documented by a staff member and the handler. For each visit, the therapy dogs were at the hospital on average 47 min and visited with nine people. There was significant correlation (P = 0.02) between the owner's perceived stress of his or her therapy dog and the dog's salivary cortisol concentrations. The handlers noted medium to high stress, and those dogs had higher cortisol concentrations post-visit. There was no significant difference in salivary cortisol for the handler and therapy dog over the course of the three visits and comparing pre- and post-visit. Overall, the dogs displayed mixed behaviors, with the three most reported being panting, lip licking, and yawning. However, salivary cortisol results suggest that the handlers and therapy dogs maintained their welfare state throughout the visits.
When Couches Have Eyes: The Effect of Visual Context on Children's Reference Processing

We examined the effects of semantic and visual cues to animacy on children's and adults' interpretation of ambiguous pronouns, using the visual world paradigm. Participants listened to sentences with object relative clauses that varied the animacy of potential referents, followed by test sentences beginning with a referentially ambiguous subject pronoun he. Participants viewed images of the referents, with semantically inanimate objects (e.g., a TV) shown with or without added facial features. Results from offline verbal report and online gaze data revealed consistent effects of both semantic animacy and visual context on pronoun resolution in both groups: There was a preference for semantically animate referents as antecedent, but this preference decreased or disappeared when semantically inanimate referents had facial features. The results indicate that the use of animacy as a linguistic cue is flexible and responsive to the visual context. They further suggest that like adults (Nieuwland and Van Berkum, 2006), 4-year-olds can already use fictional, here visual, context to adjust their online and offline language comprehension preferences.
Effects of Formica podzolica ant colonies on soil moisture, nitrogen, and plant communities near nests

1. Ants are widely regarded as ‘ecosystem engineers’ because their nest construction and contributions to nutrient cycling change the biological, chemical, and physical properties of the soil around their nests. Despite increasing attention to ant manipulation of soil ecosystems, the extent to which many common species influence soil properties, as well as nutrient uptake and community composition of plants near nests, is still unknown.
Whole-Genome Sequence of Fluoroquinolone-Resistant Escherichia coli HUE1, Isolated in Hokkaido, Japan

We report the complete genome sequence of Escherichia coli strain HUE1, isolated from the urinary catheter of a female patient, showing fluoroquinolone resistance without quinolone resistance-determining region mutations. To facilitate the exploration of the molecular characteristics of HUE1, the whole genome was sequenced using long- and short-read platforms. ABSTRACT We report the complete genome sequence of Escherichia coli strain HUE1, isolated from the urinary catheter of a female patient, showing fluoroquinolone resistance without quinolone resistance-determining region mutations. To facilitate the exploration of the molecular characteristics of HUE1, the whole genome was sequenced using long- and short-read platforms.
Metagenomic Analysis of the Microbial Diversity in Solid Waste from Okhla Landfill, New Delhi, India

The Okhla landfill site is consistently in the news for pollution levels higher than the city average. Here, we report the taxonomic and functional characterization of the microbial diversity of Okhla landfill solid waste. The metagenome analyses revealed the microbial and metabolic diversity of the site. ABSTRACT The Okhla landfill site is consistently in the news for having pollution levels higher than the city average. Here, we report the taxonomic characterization of the microbial diversity of Okhla landfill solid waste. The metagenome analyses revealed the microbial and metabolic diversity of the site.
(f, Γ)-Divergences: Interpolating between f-Divergences and Integral Probability Metrics

We develop a rigorous and general framework for constructing information-theoretic divergences that subsume both $f$-divergences and integral probability metrics (IPMs), such as the $1$-Wasserstein distance. We prove under which assumptions these divergences, hereafter referred to as $(f,\Gamma)$-divergences, provide a notion of `distance' between probability measures and show that they can be expressed as a two-stage mass-redistribution/mass-transport process. The $(f,\Gamma)$-divergences inherit features from IPMs, such as the ability to compare distributions which are not absolutely continuous, as well as from $f$-divergences, namely the strict concavity of their variational representations and the ability to control heavy-tailed distributions for particular choices of $f$. When combined, these features establish a divergence with improved properties for estimation, statistical learning, and uncertainty quantification applications. Using statistical learning as an example, we demonstrate their advantage in training generative adversarial networks (GANs) for heavy-tailed, not-absolutely continuous sample distributions and we also show improved performance and stability over gradient-penalized Wasserstein GAN in image generation.
An electrophysiological investigation of the extrinsic modulation of ventral pallidum neurons by dopamine and serotonin

The ventral pallidum (VP) is a key output structure of the basal ganglia and has multiple connections with cortical and limbic regions. The VP is modulated by extrinsic neurotransmitters, including dopamine and serotonin, but the cellular mechanisms underlying this modulation are only partially understood. This thesis describes an in vitro electrophysiological investigation of such extrinsic modulation employing extracellular multi electrode recordings of the VP and pharmacological manipulations. Our data provide novel information on how dopamine modulates VP neurons acting both pre- and post-synaptically. Presynaptic excitatory effects of dopamine are mediated by D1-like and D2-like receptors, through effects on glutamate release and subsequently ionotropic and metabotropic glutamate receptor activation. Postsynaptic, direct effects are mediated by D2-like receptors and induce decreases in firing frequency within the VP. Our data identifies two populations of neurons in the VP, which can be consistently separated by their spike half-width profile and their responses to D2-like receptor agonists. With regard to serotonin, both excitatory and inhibitory responses to its application were observed in the VP. Our data suggests that excitatory effects of Serotonin (5HT) are presynaptic, while the inhibitory responses to 5HT are postsynaptic, direct effects. Our data also suggest that 5HT1a, 5HT5A and 5HT7 receptors are responsible for increases in firing frequency to 5HT application and 5-HT2c receptors are likely candidates for the decrease in firing frequency to 5HT application in the VP. We also investigated the effects of electric activation of NAc inputs to the VP. Our data are consistent with the literature, showing that NAc inputs inhibit VP neurons. Overall, these results cast light on the cellular mechanism by which dopamine and serotonin modulate VP neurons and have important implications for our understanding of the role the VP plays in reward processing and related dysfunctions.
Character-level Representations Still Improve Semantic Parsing in the Age of BERT

We combine character-level and contextual language model representations to improve performance on Discourse Representation Structure parsing. Character representations can easily be added in a sequence-to-sequence model in either one encoder or as a fully separate encoder, with improvements that are robust to different language models, languages and data sets. For English, these improvements are larger than adding individual sources of linguistic information or adding non-contextual embeddings. A new method of analysis based on semantic tags demonstrates that the character-level representations improve performance across a subset of selected semantic phenomena.
Risk Factors of Stenotrophomonas maltophilia Blood Stream Infections: Comparison With Other Gram-Negative Blood Stream Infections in Children

Supplemental Digital Content is available in the text. Background: Stenotrophomonas maltophilia, is a nonfermentative, aerobic, Gram-negative bacilli which is intrinsically resistance to several antibiotics. Treatment options for this bacteria are quite different from the other Gram-negative bacilli, which can represent a therapeutic challenge. To initiate appropriate empiric treatment and to reduce mortality, differentiation of S. maltophilia from other Gram-negative bacteria is critically important. The aim of this study is to distinguish the risk factors of S. maltophilia blood stream infections (BSI) from other Gram-negative BSI. Methods: This was a retrospective, case-control study. Patients with S. maltophilia BSI were selected as cases and patients with non-S. maltophilia Gram-negative BSI were selected as controls. Demographic and clinical characteristics of patients were recorded. Results: Forty-eight cases with S. maltophilia BSI and 144 controls were enrolled in the study. Risk factors for S. maltophilia BSI compared with the control group includes prior use of antibiotics, especially carbapenem, pediatric intensive care unit stay, mechanical ventilator use, indwelling catheters and duration of hospitalization. Conclusions: Breakthrough infection by S. maltophilia can occur in severely ill patients being treated with carbapenem. In the presence of risk factors, to reduce morbidity and mortality, S. maltophilia should be kept in mind when starting empiric treatment.
Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus Hippophae (Elaeagnaceae)

Hippophae is a tree species with ecological, economic and social benefits. In this study, we assembled and annotated chloroplast genomes of sympatric Hippophae gyantsensis and H. rhamnoides subsp. yunnanensis. Their full-length are 155260 and 156415 bp, respectively. Each of them has 131 genes, comprising 85 protein-coding genes, 8 ribosomal RNA genes and 38 transfer RNA genes. After comparing the chloroplast genomes, we found 1302 base difference loci, and 63.29% are located in the intergenic region or intron sequences and 36.71% are located in the coding sequences. The SSC region has the highest mutation rate, followed by the LSC region; the IR regions have the lowest mutation rate. Among the protein-coding genes, three had a ratio of nonsynonymous to synonymous substitutions (Ka/Ks) >1 (but P values were non-significant) and 66 had Ka/Ks <1 (46 were significant). In general, the chloroplast protein-coding genes may be subject to purification selection. Among H. gyantsensis and H. rhamnoides subsp. yunnanensis chloroplast protein-coding genes, there are 20 and 16 optimal codons, respectively. Most of the optimal codons were ending with A or U, which indicates significant AT preference. It is an important reference for studies on the general characteristics and evolution of the Hippophae chloroplast genome.
Identification of the Single Nucleotide Polymorphisms Affecting Normal Phenotypic Variability in Human Craniofacial Morphology Using Candidate Gene Approach

There is a remarkable variety of human facial appearances, almost exclusively the result of genetic differences, as exemplified by the striking resemblance of identical twins. Despite intensive research on the genetics of craniofacial morphology using animal models and human craniofacial syndromes, the genetic variation that underpins normal human facial appearance is still largely elusive. As a part of efforts on detecting genomic variants affecting normal craniofacial appearance, we have implemented a targeted candidate gene approach by selecting 1,319 single nucleotide polymorphisms (SNPs) in over 170 candidate genes and intergenic regions. This list has been further expanded with additional 4,732 tag polymorphisms, representing extended haplotype. All the markers were genotyped in 587 DNA samples using a massively parallel sequencing approach. We used 3-dimentional (3D) facial scans and direct cranial measurements to calculate 104 craniofacial anthropometric distances, which were analysed for associations with 2,332 polymorphisms. An application of a Bonferroni corrected genome wide significance threshold produced associations between six SNPs and five craniofacial traits. Specifically, significant associations of nasal width with rs8035124 (15q26.1), cephalic index with rs16830498 (2q23.3), nasal index with rs37369 (5q13.2), transverse nasal prominence angle with rs59037879 (10p11.23) and rs10512572 (17q24.3), and a composite trait represented by a principal component with rs37369 (5p13.2) and rs390345 (14q31.3) were observed. Due to over-conservative nature of the Bonferroni correction, we also report the associations that reached the traditional genome-wide p-value threshold (< 5.00E-08) as suggestive. Based on the genome-wide significance threshold, 8 craniofacial phenotypes demonstrated significant and mostly novel associations with 33 intergenic and extragenic SNPs, potentially involved in gene regulation. This study identified a large number of genetic variants associated with normal craniofacial morphology variation, including confirmation of the two previously reported genes. These results enhance our understanding of the craniofacial genetics affecting normal craniofacial appearance and will be of particular value for clinical diagnostics and forensic molecular phenotyping.
Effect of chitosan on production performance of feedlot lambs

Abstract Intake, digestibility, nitrogen (N) balance, microbial protein synthesis, weight gain, yields of the main commercial cuts and carcass morphometric measurements were evaluated in lambs fed diets containing different levels of chitosan. Sixty Santa Inês crossbred sheep with an average body weight (BW) of 24 ± 2.2 kg were assigned to three treatments (diets containing 0, 136 or 272 mg chitosan/kg BW) in a completely randomized design. There was no effect of chitosan on dry matter (DM) intake. Ingested and retained N showed a quadratic response, with the highest values estimated at the chitosan levels of 142 and 152 mg/kg BW, respectively. Similar to N balance, microbial protein synthesis showed the same quadratic response, in which the level of 136 mg/kg BW resulted in higher synthesis when compared with the other levels. No effect of chitosan was detected on average daily gain, final weight, or carcass variables (hot carcass weight, cold carcass weight, yield of commercial cuts and morphometric measurements of the carcass). Conformation, visceral fat content and fatness of carcasses were also not altered by the use of chitosan. Chitosan improves the digestibility of DM, crude protein and neutral detergent fibre, and increases N balance and microbial protein synthesis but does not change the production performance of feedlot lambs.
Precursor microRNA Identification Using Deep Convolutional Neural Networks

Precursor microRNA (pre-miRNA) identification is the basis for identifying microRNAs (miRNAs), which have important roles in post-transcriptional regulation of gene expression. In this paper, we propose a deep learning method to identify whether a small non-coding RNA sequence is a pre-miRNA or not. We outperform state-of-the-art methods on three benchmark datasets, namely the human, cross-species, and new datasets. The key of our method is to use a matrix representation of predicted secondary structure as input to a 2D convolutional network. The neural network extracts optimized features automatically instead of using a large number of handcrafted features as most existing methods do. Code and results are available at https://github.com/peace195/miRNA-identification-conv2D.
Modeling microbial communities using biochemical resource allocation analysis

To understand the functioning and dynamics of microbial communities remains a fundamental challenge at the forefront of current biology. To tackle this challenge, the construction of computational models of interacting microbes is an indispensable tool. Currently, however, there is a large chasm between ecologically-motivated descriptions of microbial growth used in ecosystems simulations, and detailed metabolic pathway and genome-based descriptions developed within systems and synthetic biology. Here, we seek to demonstrate how current biochemical resource allocation models of microbial growth offer the potential to advance ecosystem simulations and their parameterization. In particular, recent work on quantitative microbial growth and cellular resource allocation allow us to formulate mechanistic models of microbial growth that are physiologically meaningful while remaining computationally tractable. Biochemical resource allocation models go beyond Michaelis-Menten and Monod-type growth models, and allow to account for emergent properties that underlie the remarkable plasticity of microbial growth. We exemplify our approach using a coarse-grained model of cyanobacterial phototrophic growth, and demonstrate how the model allows us to represent physiological acclimation to different environments, co-limitation of growth by several nutrients, as well as emergent switches between alternative nutrient sources. Our approach has implications for building models of microbial communities to understand their interactions, dynamics and response to environmental changes.