Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Control of Water Use Efficiency and Leaf Carbon Isotope Discrimination in Sunflower (Helianthus annuus L.) Subjected to Two Drought Scenarios

High water use efficiency (WUE) can be achieved by coordination of biomass accumulation and water consumption. WUE is physiologically and genetically linked to carbon isotope discrimination (CID) in leaves of plants. A population of 148 recombinant inbred lines (RILs) of sunflower derived from a cross between XRQ and PSC8 lines was studied to identify quantitative trait loci (QTL) controlling WUE and CID, and to compare QTL associated with these traits in different drought scenarios. We conducted greenhouse experiments in 2011 and 2012 by using 100 balances which provided a daily measurement of water transpired, and we determined WUE, CID, biomass and cumulative water transpired by plants. Wide phenotypic variability, significant genotypic effects, and significant negative correlations between WUE and CID were observed in both experiments. A total of nine QTL controlling WUE and eight controlling CID were identified across the two experiments. A QTL for phenotypic response controlling WUE and CID was also significantly identified. The QTL for WUE were specific to the drought scenarios, whereas the QTL for CID were independent of the drought scenarios and could be found in all the experiments. Our results showed that the stable genomic regions controlling CID were located on the linkage groups 06 and 13 (LG06 and LG13). Three QTL for CID were co-localized with the QTL for WUE, biomass and cumulative water transpired. We found that CID and WUE are highly correlated and have common genetic control. Interestingly, the genetic control of these traits showed an interaction with the environment (between the two drought scenarios and control conditions). Our results open a way for breeding higher WUE by using CID and marker-assisted approaches and therefore help to maintain the stability of sunflower crop production.
Neuroanatomical correlates of temperament in early adolescents.

OBJECTIVE Temperament refers to enduring behavioral characteristics that underpin individual differences in human behavior, including risk for psychopathology. Research attempting to investigate the neurobiological basis of temperament represents an important step toward elucidating the biological mechanisms underlying these individual differences. In the present study, we examined the relation between four core temperament dimensions and anatomically defined regions of the limbic and prefrontal cortices. METHOD We used a cross-sectional design to examine a large sample (N = 153; mean age 12.6 years, SD 0.4, range 11.4-13.7) of healthy early adolescents who were selected from a larger sample to maximize variation in temperament. The main outcome measures were psychometric measures of temperament (four factors: effortful control, negative affectivity, surgency, and affiliativeness) based on the Early Adolescent Temperament Questionnaire-Revised, and volumetric measures of a priori brain regions of interest (anterior cingulate cortex [ACC], orbitofrontal cortex, amygdala, and hippocampus). RESULTS We found regional brain volumes to account for small but significant amounts of the variance in self-reported temperament scores. Specifically, higher effortful control was associated with larger volume of the left orbitofrontal cortex and hippocampus. Higher negative affectivity was associated with smaller volume of the left dorsal paralimbic relative to limbic portion of the ACC. Higher affiliativeness was associated with larger volume of the right rostral/ventral limbic portion of the ACC. Affiliativeness and surgency also showed a number of female-specific associations, primarily involving the rostral/ventral ACC. CONCLUSIONS Our results provide support for a neuroanatomical basis for individual differences in temperament and have implications for understanding the neurobiological mechanisms underlying the development of a number of psychiatric disorders.
Multiomics Integration Reveals the Landscape of Prometastasis Metabolism in Hepatocellular Carcinoma*

The systematic investigation of gene mutation and expression is important to discover novel biomarkers and therapeutic targets in cancers. Here, we integrated genomics, transcriptomics, proteomics, and metabolomics to analyze three hepatocellular carcinoma (HCC) cell lines with differential metastatic potentials. The results revealed the profile of the prometastasis metabolism potentially associated with HCC metastasis. The multiomic analysis identified 12 genes with variations at multiple levels from three metabolic pathways, including glycolysis, starch, and sucrose metabolism, and glutathione metabolism. Furthermore, uridine diphosphate (UDP)-glucose pyrophosphorylase 2 (UGP2), was observed to be persistently up-regulated with increased metastatic potential. UGP2 overexpression promoted cell migration and invasion and enhanced glycogenesis in vitro. The role of UGP2 in metastasis was further confirmed using a tumor xenograft mouse model. Taken together, the compendium of multiomic data provides valuable insights in understanding the roles of shifted cellular metabolism in HCC metastasis.
Impact of “a” determinant mutations on detection of hepatitis B surface antigen (HBsAg) in HBV strains from Chinese patients with occult hepatitis B

This study was designed to detect mutations that occur within the “a” determinant in the S gene of the hepatitis B virus (HBV) in patients with occult hepatitis B (OHB), and to analyze the influence of these mutations on expression and reactivity of the hepatitis B surface antigen (HBsAg). Twenty‐three certified OHB samples were compared to 32 HBsAg positive samples from patients with chronic hepatitis B. The median HBV DNA levels in the OHB group were significantly lower than those in the control group (P < 0.0001). Mutations within the “a” determinant were analyzed by gene amplification and sequencing. This revealed mixed infections in which clones within a sample displayed either different mutations or mutations in association with clones that exhibited wild type amino acid patterns. Sequencing analysis also showed a significant difference between the proportions of amino acid mutations observed in the OHB and control groups. Seven recombinant S (rS) proteins with corresponding OHB mutations and three wild type alleles were expressed and purified in the Pichia pastoris expression system to preserve conformational attributes, and their reactivity analyzed using six commercial HBsAg assays. The OHB sera were HBsAg nonreactive while the rS proteins with corresponding OHB mutations were universally reactive. Thus, we postulate that the reduced binding affinity between mutated HBsAg and its antibody may not be as important in defining OHB as is the effect of specific mutations in the preS/S region of the genome that affect the synthesis and secretion of the S protein and/or the virion.
Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach

Spores of Bacillus cereus pose a threat to food safety due to their high resistance to the heat or acid treatments commonly used to make food microbiologically safe. Spores may survive these treatments and later resume growth either on foodstuffs or, after ingestion, upon entering the gut they are capable of producing toxins, which cause either vomiting or diarrhea. The outer layers of the spore, the spore coat and exosporium, consist primarily of proteins that may serve as potential biomarkers for detection. The major morphogenetic protein CotE is important for correct assembly and attachment of the outermost layer, the exosporium, and by extension retention of many proteins. However, characterization of the proteins affected by deletion of CotE has been limited to electrophoretic patterns. Here we report the effect of CotE deletion on the insoluble fraction of the spore proteome through liquid chromatography–Fourier transform tandem mass spectrometry (LC–FTMS/MS) analysis. A total of 560 proteins have been identified in both mutant and wild-type spore coat isolates. A further 163 proteins were identified exclusively in wild-type spore isolates indicating that they are dependent on CotE for their association with the spore. Several of these are newly confirmed as associated with the exosporium, namely BC_2569 (BclF), BC_3345, BC_2427, BC_2878, BC_0666, BC_2984, BC_3481, and BC_2570. A total of 153 proteins were only identified in ΔCotE spore isolates. This was observed for proteins that are known or likely to be interacting with or are encased by CotE. Crucial spore proteins were quantified using a QconCAT reference standard, the first time this was used in a biochemically heterogeneous system. This allowed us to determine the absolute abundance of 21 proteins, which spanned across three orders of magnitude and together covered 5.66% ± 0.51 of the total spore weight. Applying the QconCAT methodology to the ΔCotE mutant allowed us to quantify 4.13% ± 0.14 of the spore total weight and revealed a reduction in abundance for most known exosporium associated proteins upon CotE deletion. In contrast, several proteins, either known or likely to be interacting with or encased by CotE (i.e., GerQ), were more abundant. The results obtained provide deeper insight into the layered spore structure such as which proteins are exposed on the outside of the spore. This information is important for developing detection methods for targeting spores in a food safety setting. Furthermore, protein stoichiometry and determination of the abundance of germination mediating enzymes provides useful information for germination and outgrowth model development.
Convergent behavioral and corticolimbic connectivity evidence of a negativity bias in children and adolescents

Abstract Individuals differ in their tendency to perceive negativity in ambiguous situations or facial expressions. Prior research demonstrates that this so-called “negativity bias” is exaggerated in children; for instance, when they rate the emotional content of neutral facial expressions. However, neutral faces are frequently used as a baseline condition in pediatric emotion processing studies, as they are thought to be emotionally neutral. Here, we present data that challenge that notion. We demonstrate that children and adolescents rate neutral faces, particularly of adults, as negative, similar to ratings elicited by angry faces. In addition, we found a lack of age-related decrease in reaction time for neutral adult faces, suggesting that these stimuli remain salient across development. Demonstrating the relevance of individual differences, higher negativity bias was associated with lower self-reported reward sensitivity and increased functional connectivity of the amygdala. Together, these findings indicate that neutral faces are not perceived as emotionally neutral in children, thus discouraging their use as baseline condition in pediatric research. These data also offer a potential neurobiological substrate of the negativity bias in children. The link to corticolimbic emotion-processing circuitry and affective experience implies that exaggerations in these biases may be relevant for the development of emotional psychopathology.
Generalized Frequency Division Multiplexing with Index Modulation

Generalized frequency division multiplexing (GFDM) is a promising non-orthogonal multicarrier transmission scheme which has recently received a great deal of attention towards future fifth generation (5G) wireless networks. It overcomes the limitations of orthogonal frequency division multiplexing (OFDM) while preserving most of the advantages of it. On the other hand, index modulation (IM) has the potential to provide a flexible system design with adjustable number of active subcarriers as well as significant bit error rate (BER) performance improvement for multicarrier systems. In this paper, we propose the combined application of GFDM and IM techniques. We present the GFDM-IM system model and evaluate its error performance by comparing to classical GFDM and OFDM-IM for Rayleigh multipath fading channels. It is shown via computer simulations that the GFDM-IM system achieves signicantly better error performance than classical GFDM due to the information bits carried in the spatial domain by the indices of active GFDM subcarriers.
Opioid-Induced Mitogen-Activated Protein Kinase Signaling in Rat Enteric Neurons following Chronic Morphine Treatment

Opioids, acting at μ opioid receptors, are commonly used for pain management. Chronic opioid treatment induces cellular adaptations, which trigger long-term side effects, including constipation mediated by enteric neurons. We tested the hypothesis that chronic opioid treatment induces alterations of μ opioid receptor signaling in enteric neurons, which are likely to serve as mechanisms underlying opioid-induced constipation. In cultured rat enteric neurons, either untreated (naïve) or exposed to morphine for 4 days (chronic), we compared the effect of morphine and DAMGO (D-Ala2,MePhe4,Gly-ol5 enkephalin) on μ opioid receptor internalization and downstream signaling by examining the activation of the mitogen-activated protein kinase/extracellular signal-regulated kinases 1 and 2 (MAPK/ERK) pathway, cAMP accumulation and transcription factor cAMP Response Element-Binding protein (CREB) expression. μ opioid receptor internalization and MAPK/ERK phosphorylation were induced by DAMGO, but not morphine in naïve neurons, and by both opioids in chronic neurons. MAPK/ERK activation was prevented by the receptor antagonist naloxone, by blocking receptor trafficking with hypertonic sucrose, dynamin inhibitor, or neuronal transfection with mutated dynamin, and by MAPK inhibitor. Morphine and DAMGO inhibited cAMP in naïve and chronic enteric neurons, and induced desensitization of cAMP signaling. Chronic morphine treatment suppressed desensitization of cAMP and MAPK signaling, increased CREB phosphorylation through a MAPK/ERK pathway and induced delays of gastrointestinal transit, which was prevented by MAPK/ERK blockade. This study showed that opioids induce endocytosis- and dynamin-dependent MAPK/ERK activation in enteric neurons and that chronic morphine treatment triggers changes at the receptor level and downstream signaling resulting in MAPK/ERK-dependent CREB activation. Blockade of this signaling pathway prevents the development of gastrointestinal motility impairment induced by chronic morphine treatment. These findings suggest that alterations in μ opioid receptor downstream signaling including MAPK/ERK pathway in enteric neurons chronically treated with morphine contribute to the development of opioid-induced constipation.
Experimental Investigation of Friction and Wear Properties for Glass/Carbon Hybrid Fiber Reinforced with Epoxy Resin

Friction and wear properties of glass/carbon hybrid fiber weave reinforced with epoxy resin are reported in this experimental study. The tribological properties are investigated using a pin-on-disk test apparatus which measures coefficient friction and wear rate. The experiments are conducted at various loads and sliding distance at constant velocity 5m/s, the purpose is to compare the performance at different sliding conditions. It is found that the wear rate is increased by increasing the carbon content, but the co-efficient of friction decreases by increasing the carbon percentage in the composite.
Successful peripheral blood stem cell mobilization with a cost-efficient single fixed-dose plerixafor schedule in poor mobilizers

Abstract Plerixafor, although costly, is added to mobilizing chemotherapy and G-CSF to overcome poor stem cell mobilization. We demonstrate that it can be safely administered mostly once as a single dose in preemptive and rescue settings, leading to apheresis yields of >2 and >4×106 CD34 + cells/kg body weight (bw) in 83% and 48%, respectively. Of note, 35/46 (76%) patients showed a substantial benefit with increased peripheral blood (PB) CD34 + cells prior to apheresis (8.84 vs. 1.72/μl, p < .001), and 5-fold increased CD34 + cells collected per single apheresis (2.25 vs. 0.43 × 106 CD34+/kg bw, respectively, p < .001). Patients profiting most (76%) vs. less (24%) had >5 vs. <5/μl PB CD34 + cells before plerixafor application, respectively, thus careful patient selection in the latter group is advised. To the best of our knowledge, this is the first report demonstrating that favorable apheresis results can be obtained using this cost-efficient, single fixed-dose plerixafor schedule.
The Altitudinal Patterns of Leaf C∶N∶P Stoichiometry Are Regulated by Plant Growth Form, Climate and Soil on Changbai Mountain, China

Understanding the geographic patterns and potential drivers of leaf stoichiometry is critical for modelling the nutrient fluxes of ecosystems and to predict the responses of ecosystems to global changes. This study aimed to explore the altitudinal patterns and potential drivers of leaf C∶N∶P stoichiometry. We measured the concentrations of leaf C, N and P in 175 plant species as well as soil nutrient concentrations along an altitudinal transect (500–2300 m) on the northern slope of Changbai Mountain, China to explore the response of leaf C∶N∶P stoichiometry to plant growth form (PGF), climate and soil. Leaf C, N, P and C∶N∶P ratios showed significant altitudinal trends. In general, leaf C and C∶N∶P ratios increased while leaf N and P decreased with elevation. Woody and herbaceous species showed different responses to altitudinal gradients. Trees had the largest variation in leaf C, C∶N and C∶P ratios, while herbs showed the largest variation in leaf N, P and N∶P ratio. PGF, climate and soil jointly regulated leaf stoichiometry, explaining 17.6% to 52.1% of the variation in the six leaf stoichiometric traits. PGF was more important in explaining leaf stoichiometry variation than soil and climate. Our findings will help to elucidate the altitudinal patterns of leaf stoichiometry and to model ecosystem nutrient cycling.
Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity

Significance In the 15 y since metabolite-binding riboswitches were first experimentally validated, only 4 examples of riboswitch classes with altered specificity have been confirmed by experiments out of ∼30 distinct structural architectures. In contrast, evolutionary changes in ligand specificity of proteins are routinely reported. To further investigate the propensity for natural adaptation of riboswitch specificity, we developed a structural bioinformatics method to systematically search for variant riboswitches with altered ligand recognition. This search method yielded evidence for altered specificity within five riboswitch classes, including validation of a second riboswitch class that senses 2′-deoxyguanosine. Riboswitches are RNAs that form complex, folded structures that selectively bind small molecules or ions. As with certain groups of protein enzymes and receptors, some riboswitch classes have evolved to change their ligand specificity. We developed a procedure to systematically analyze known riboswitch classes to find additional variants that have altered their ligand specificity. This approach uses multiple-sequence alignments, atomic-resolution structural information, and riboswitch gene associations. Among the discoveries are unique variants of the guanine riboswitch class that most tightly bind the nucleoside 2′-deoxyguanosine. In addition, we identified variants of the glycine riboswitch class that no longer recognize this amino acid, additional members of a rare flavin mononucleotide (FMN) variant class, and also variants of c-di-GMP-I and -II riboswitches that might recognize different bacterial signaling molecules. These findings further reveal the diverse molecular sensing capabilities of RNA, which highlights the potential for discovering a large number of additional natural riboswitch classes.
Epilepsy, antiepileptic drugs, and serious transport accidents

Objectives To investigate the association between epilepsy and antiepileptic drugs and serious transport accidents requiring emergency care or resulting in death. Methods We identified 29,220 individuals 18 years or older with epilepsy without cerebral palsy or intellectual disability and 267,637 matched controls using Swedish registers. This nationwide cohort was followed from 2006 to 2013 for serious transport accidents. We used Cox regression to analyze the risk of serious transport accidents between individuals with epilepsy and matched controls, and then stratified Cox regression to compare the risk during periods of medication with the risk during nonmedication period within the same individual with epilepsy. We adjusted for civil status, employment, education, living area, psychiatric disorders prior to the start of follow-up, and psychotropic medication. Results Compared to matched controls, individuals with epilepsy were at increased risk of serious transport accidents (hazard ratio [HR] 1.37; 95% confidence interval [CI] 1.29–1.46). There were increased risks of pedestrian accidents (HR 2.24, 95% CI 1.69–2.97), bicycle accidents (HR 1.68, 95% CI 1.49–1.89) and car accidents (HR 1.31, 95% CI 1.19–1.44). However, among patients with a diagnosis of epilepsy, use of antiepileptic drugs did not influence the risk of serious transport accidents in population-level comparisons (HR 0.97; 95% CI 0.85–1.11) or within-individual comparisons (HR 0.99; 95% CI 0.69–1.42). Conclusion Serious transportation accidents were more common in individuals with epilepsy, but this risk was independent of use of antiepileptic drugs.
Liganded Peroxisome Proliferator-Activated Receptors (PPARs) Preserve Nuclear Histone Deacetylase 5 Levels in Endothelin-Treated Sprague-Dawley Rat Cardiac Myocytes

Ligand activation of peroxisome proliferator-activated receptors (PPARs) prevents cardiac myocyte hypertrophy, and we previously reported that diacylglycerol kinase zeta (DGKζ) is critically involved. DGKζ is an intracellular lipid kinase that catalyzes phosphorylation of diacylglycerol; by attenuating DAG signaling, DGKζ suppresses protein kinase C (PKC) and G-protein signaling. Here, we investigated how PPAR-DGKζ signaling blocks activation of the hypertrophic gene program. We focused on export of histone deacetylase 5 (HDAC5) from the nucleus, a key event during hypertrophy, since crosstalk occurs between PPARs and other members of the HDAC family. Using cardiac myocytes isolated from Sprague-Dawley rats, we determined that liganded PPARs disrupt endothelin-1 (ET1)-induced nuclear export of HDAC5 in a manner that is dependent on DGKζ. When DGKζ-mediated PKC inhibition was circumvented using a constitutively-active PKCε mutant, PPARs failed to block ET1-induced nuclear retention of HDAC5. Liganded PPARs also prevented (i) activation of protein kinase D (the downstream effector of PKC), (ii) HDAC5 phosphorylation at 14-3-3 protein chaperone binding sites (serines 259 and 498), and (iii) physical interaction between HDAC5 and 14-3-3, all of which are consistent with blockade of nucleo-cytoplasmic shuttling of HDAC5. Finally, the ability of PPARs to prevent neutralization of HDAC5 activity was associated with transcriptional repression of hypertrophic genes. This occurred by first, reduced MEF2 transcriptional activity and second, augmented deacetylation of histone H3 associated with hypertrophic genes expressing brain natriuretic peptide, β-myosin heavy chain, skeletal muscle α-actin, and cardiac muscle α-actin. Our findings identify spatial regulation of HDAC5 as a target for liganded PPARs, and to our knowledge, are the first to describe a mechanistic role for nuclear DGKζ in cardiac myocytes. In conclusion, these results implicate modulation of HDAC5 as a mechanism by which liganded PPARs suppress the hypertrophic gene program.