Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic Pathways Involved in Cold Acclimation Identified by Integrated Analysis of Metabolites and Transcripts Regulated by DREB1A and DREB2A1[W][OA]

DREB1A/CBF3 and DREB2A are transcription factors that specifically interact with a cis-acting dehydration-responsive element (DRE), which is involved in cold- and dehydration-responsive gene expression in Arabidopsis (Arabidopsis thaliana). Overexpression of DREB1A improves stress tolerance to both freezing and dehydration in transgenic plants. In contrast, overexpression of an active form of DREB2A results in significant stress tolerance to dehydration but only slight tolerance to freezing in transgenic plants. The downstream gene products for DREB1A and DREB2A are reported to have similar putative functions, but downstream genes encoding enzymes for carbohydrate metabolism are very different between DREB1A and DREB2A. We demonstrate that under cold and dehydration conditions, the expression of many genes encoding starch-degrading enzymes, sucrose metabolism enzymes, and sugar alcohol synthases changes dynamically; consequently, many kinds of monosaccharides, disaccharides, trisaccharides, and sugar alcohols accumulate in Arabidopsis. We also show that DREB1A overexpression can cause almost the same changes in these metabolic processes and that these changes seem to improve freezing and dehydration stress tolerance in transgenic plants. In contrast, DREB2A overexpression did not increase the level of any of these metabolites in transgenic plants. Strong freezing stress tolerance of the transgenic plants overexpressing DREB1A may depend on accumulation of these metabolites.
Brain Involvement in Myotonic Dystrophy Type 1: A Morphometric and Diffusion Tensor Imaging Study with Neuropsychological Correlation

Objective Myotonic dystrophy type 1 (DM1), the most prevalent inherited neuromuscular disease in adults, is a genetic multisystem disorder with a well-established but not well-characterized cerebral involvement. The aim of this study was to evaluate the presence of white matter and gray matter abnormalities in DM1 patients and to investigate their relationship with neurocognitive dysfunction. Methods A total of 42 DM1 patients and 42 healthy controls were included in the study. Clinical, cognitive, and magnetic resonance imaging evaluations, including the use of structural and diffusion tensor imaging (DTI) techniques, were performed. White matter lesion (WML) load, volumetric analysis, and diffusivity changes were assessed and correlated with clinical and neuropsychological test findings. Results WMLs were significantly more frequent in DM1 patients (p < .001), and anterior temporal lobe lesions were only found in the patient group. Global and regional cortical volume loss and corpus callosum atrophy were found. Diffuse white matter DTI abnormalities, including fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity were observed with sparing of the internal capsule. Subcortical structures showed volume loss and increased median diffusivity. Neuropsychological evaluation showed significant impairment in several cognitive functions, but only visuospatial impairment was correlated with white matter abnormalities and cortical atrophy. Daytime sleepiness was associated with WML and ventral diencephalon and pallidum volume loss. Conclusion DM1 produces a widespread involvement of white matter and gray matter, including cortical and subcortical structures. These structural abnormalities are involved in the progressive neuropsychological functional impairment in these patients.
Combining decidability paradigms for existential rules. Theory and Practice of Logic Programming - CORRIGENDUM

Figure 3 was left out in the article (Gottlob et al. 2013). The figure that is given there as figure 3 should in fact be figure 4. Further, the reference to figure 3 on the 4 th line of page 889 should be a reference to figure 4. The correct figure 3 (missing in the paper) is supplied below. We apologise for this error.
Loss of Halophytism by Interference with SOS1 Expression1[W][OA]

The contribution of SOS1 (for Salt Overly Sensitive 1), encoding a sodium/proton antiporter, to plant salinity tolerance was analyzed in wild-type and RNA interference (RNAi) lines of the halophytic Arabidopsis (Arabidopsis thaliana)-relative Thellungiella salsuginea. Under all conditions, SOS1 mRNA abundance was higher in Thellungiella than in Arabidopsis. Ectopic expression of the Thellungiella homolog ThSOS1 suppressed the salt-sensitive phenotype of a Saccharomyces cerevisiae strain lacking sodium ion (Na+) efflux transporters and increased salt tolerance of wild-type Arabidopsis. thsos1-RNAi lines of Thellungiella were highly salt sensitive. A representative line, thsos1-4, showed faster Na+ accumulation, more severe water loss in shoots under salt stress, and slower removal of Na+ from the root after removal of stress compared with the wild type. thsos1-4 showed drastically higher sodium-specific fluorescence visualized by CoroNa-Green, a sodium-specific fluorophore, than the wild type, inhibition of endocytosis in root tip cells, and cell death in the adjacent elongation zone. After prolonged stress, Na+ accumulated inside the pericycle in thsos1-4, while sodium was confined in vacuoles of epidermis and cortex cells in the wild type. RNAi-based interference of SOS1 caused cell death in the root elongation zone, accompanied by fragmentation of vacuoles, inhibition of endocytosis, and apoplastic sodium influx into the stele and hence the shoot. Reduction in SOS1 expression changed Thellungiella that normally can grow in seawater-strength sodium chloride solutions into a plant as sensitive to Na+ as Arabidopsis.
The Role of Oxophytodienoate Reductases in the Detoxification of the Explosive 2,4,6-Trinitrotoluene by Arabidopsis1[W][OA]

The explosive 2,4,6-trinitrotoluene (TNT) is a significant environmental pollutant that is both toxic and recalcitrant to degradation. Phytoremediation is being increasingly proposed as a viable alternative to conventional remediation technologies to clean up explosives-contaminated sites. Despite the potential of this technology, relatively little is known about the innate enzymology of TNT detoxification in plants. To further elucidate this, we used microarray analysis to identify Arabidopsis (Arabidopsis thaliana) genes up-regulated by exposure to TNT and found that the expression of oxophytodienoate reductases (OPRs) increased in response to TNT. The OPRs share similarity with the Old Yellow Enzyme family, bacterial members of which have been shown to transform explosives. The three predominantly expressed forms, OPR1, OPR2, and OPR3, were recombinantly expressed and affinity purified. Subsequent biochemical characterization revealed that all three OPRs are able to transform TNT to yield nitro-reduced TNT derivatives, with OPR1 additionally producing the aromatic ring-reduced products hydride and dihydride Meisenheimer complexes. Arabidopsis plants overexpressing OPR1 removed TNT more quickly from liquid culture, produced increased levels of transformation products, and maintained higher fresh weight biomasses than wild-type plants. In contrast, OPR1,2 RNA interference lines removed less TNT, produced fewer transformation products, and had lower biomasses. When grown on solid medium, two of the three OPR1 lines and all of the OPR2-overexpressing lines exhibited significantly enhanced tolerance to TNT. These data suggest that, in concert with other detoxification mechanisms, OPRs play a physiological role in xenobiotic detoxification.
Communicating terminal diagnoses to Hispanic patients

Abstract Objective: This study addressed factors physicians employ in their communication of a terminal diagnosis and a hospice referral to Hispanic patients. Method: The research method used was an exploratory qualitative in-depth semi-structured interview with thematic analysis. The interviews were with ten physicians in Central Florida. The interviews were conducted in Spanish and/or English with physicians who serve terminally ill Hispanic patients. Results: The findings provide vital information on factors that impact communication of diagnosis and hospice referral. Themes emerged relating to role of family members and end-of-life decision-making. Language barriers and limited knowledge of cultural factors and beliefs impacted communication related to end-of-life decisions. Gaps in training and education for physicians were also identified. Significance of results: These results suggest that discussing end-of-life issues with the diverse category of Hispanic patients and families will be enhanced by eliminating language barriers, increased understanding of the role of family members, and knowledge of cultural factors and beliefs related to end-of-life decisions.
Effect of Rubisco Activase Deficiency on the Temperature Response of CO2 Assimilation Rate and Rubisco Activation State: Insights from Transgenic Tobacco with Reduced Amounts of Rubisco Activase1[W][OA]

The activation of Rubisco in vivo requires the presence of the regulatory protein Rubisco activase. To elucidate its role in maintaining CO2 assimilation rate at high temperature, we examined the temperature response of CO2 assimilation rate at 380 μL L−1 CO2 concentration (A380) and Rubisco activation state in wild-type and transgenic tobacco (Nicotiana tabacum) with reduced Rubisco activase content grown at either 20°C or 30°C. Analyses of gas exchange and chlorophyll fluorescence showed that in the wild type, A380 was limited by ribulose 1,5-bisphosphate regeneration at lower temperatures, whereas at higher temperatures, A380 was limited by ribulose 1,5-bisphosphate carboxylation irrespective of growth temperatures. Growth temperature induced modest differences in Rubisco activation state that declined with measuring temperature, from mean values of 76% at 15°C to 63% at 40°C in wild-type plants. At measuring temperatures of 25°C and below, an 80% reduction in Rubisco activase content was required before Rubisco activation state was decreased. Above 35°C, Rubisco activation state decreased slightly with more modest decreases in Rubisco activase content, but the extent of the reductions in Rubisco activation state were small, such that a 55% reduction in Rubisco activase content did not alter the temperature sensitivity of Rubisco activation and had no effect on in vivo catalytic turnover rates of Rubisco. There was a strong correlation between Rubisco activase content and Rubisco activation state once Rubisco activase content was less that 20% of wild type at all measuring temperatures. We conclude that reduction in Rubisco activase content does not lead to an increase in the temperature sensitivity of Rubisco activation state in tobacco.
Cancer and post-traumatic stress disorder: Diagnosis, pathogenesis and treatment considerations

Abstract Objective: The purpose of this article was to review the literature regarding diagnosis, pathogenesis, and treatment of post-traumatic stress disorder (PTSD) associated with cancer. Method: We surveyed studies examining the validity of diagnostic scales commonly used to measure PTSD in patients with cancer. Neurobiological underpinnings of PTSD and cancer, including inflammation as the physiological mechanism linking these comorbidities, were examined. Psychopharmacologic and psychotherapeutic treatment of PTSD symptoms in patients with cancer was reviewed. In addition, potential drug–drug interactions between psychotropic medications commonly used to treat PTSD and anti-cancer agents were reviewed. Results: Multiple studies demonstrated the validity of the PTSD Checklist Civilian Version (PCL-C) in diagnosing PTSD in patients with cancer. Research has shown that PTSD as defined in DSM-IV appears to be a better model for conceptualizing distress in patients with cancer than a generalized “distress” model. Epidemiologic studies have shown an increased incidence of PTSD associated with cancer; however, literature regarding characteristics of PTSD in patients with cancer is cross-sectional in nature. Significance of results: Future research focusing on longitudinal, prospective studies to identify patients at risk, determine causal or aggravating factors, and develop preventive interventions is needed. Further study of PTSD in patients with cancer may help increase recognition of this disorder, optimize treatment, and enhance the quality of life of these individuals.
Metabolite profiling of non‐sterile rhizosphere soil

Summary Rhizosphere chemistry is the sum of root exudation chemicals, their breakdown products and the microbial products of soil‐derived chemicals. To date, most studies about root exudation chemistry are based on sterile cultivation systems, which limits the discovery of microbial breakdown products that act as semiochemicals and shape microbial rhizosphere communities. Here, we present a method for untargeted metabolic profiling of non‐sterile rhizosphere soil. We have developed an experimental growth system that enables the collection and analysis of rhizosphere chemicals from different plant species. High‐throughput sequencing of 16S rRNA genes demonstrated that plants in the growth system support a microbial rhizosphere effect. To collect a range of (a)polar chemicals from the system, we developed extraction methods that do not cause detectable damage to root cells or soil‐inhabiting microbes, thus preventing contamination with cellular metabolites. Untargeted metabolite profiling by UPLC‐Q‐TOF mass spectrometry, followed by uni‐ and multivariate statistical analyses, identified a wide range of secondary metabolites that are enriched in plant‐containing soil, compared with control soil without roots. We show that the method is suitable for profiling the rhizosphere chemistry of Zea mays (maize) in agricultural soil, thereby demonstrating the applicability to different plant–soil combinations. Our study provides a robust method for the comprehensive metabolite profiling of non‐sterile rhizosphere soil, which represents a technical advance towards the establishment of causal relationships between the chemistry and microbial composition of the rhizosphere.
Identification and characterization of the phosphatidic acid‐binding A. thaliana phosphoprotein PLDrp1 that is regulated by PLD&agr;1 in a stress‐dependent manner

Phospholipase D (PLD) and its cleavage product phosphatidic acid (PA) are crucial in plant stress-signalling. Although some targets of PLD and PA have been identified, the signalling pathway is still enigmatic. This study demonstrates that the phosphoprotein At5g39570, now called PLD-regulated protein1 (PLDrp1), from Arabidopsis thaliana is directly regulated by PLDα1. The protein PLDrp1 can be divided into two regions with distinct properties. The conserved N-terminal region specifically binds PA, while the repeat-rich C-terminal domain suggests interactions with RNAs. The expression of PLDrp1 depends on PLDα1 and the plant water status. Water stress triggers a pldα1-like phenotype in PLDrp1 mutants and induces the expression of PLDrp1 in pldα1 mutants. The regulation of PLDrp1 by PLDα1 and environmental stressors contributes to the understanding of the complex PLD regulatory network and presents a new member of the PA-signalling chain in plants.
Family members' views on the benefits of harp music vigils for terminally-ill or dying loved ones

Abstract Objectives: Music-thanatology is a palliative modality that uses harp and voice to provide bedside vigils, particularly for terminally ill or actively dying. We sought to determine the benefits of music vigils for terminally ill patients. Methods: Survey of 55 family members, whose terminally ill loved one experienced a music vigil during hospitalization, regarding effects on the patient's breathing, relaxation, comfort, pain and ability to sleep. Written comments on negative and positive results of the vigils were coded using content analysis. Results: Family members perceived that the vigils resulted in modest improvement in the patients' breathing, relaxation, comfort, and ability to sleep, with fewer positive effects on pain, and almost no negative effects. Open ended comments focused on the positive benefit in increasing calm, relaxation, comfort. Comments on the positive effects for the family were almost as common as comments on the positive results for the patient. Significance of Results: The use of music-vigils in palliative care should be investigated more extensively as our study supports that this intervention has benefits, almost no risk, minimal cost, and may improve patient-family experience of the dying process.
Concurrent isotope-assisted metabolic flux analysis and transcriptome profiling reveal responses of poplar cells to altered nitrogen and carbon supply.

Reduced nitrogen is indispensable to plants. However, its limited availability in soil combined with the energetic and environmental impacts of nitrogen fertilizers motivates research into molecular mechanisms toward improving plant nitrogen use efficiency (NUE). We performed a systems-level investigation of this problem by employing multiple 'omics methodologies on cell suspensions of hybrid poplar (Populus tremula × Populus alba). Acclimation and growth of the cell suspensions in four nutrient regimes ranging from abundant to deficient supplies of carbon and nitrogen revealed that cell growth under low-nitrogen levels was associated with substantially higher NUE. To investigate the underlying metabolic and molecular mechanisms, we concurrently performed steady-state 13 C metabolic flux analysis with multiple isotope labels and transcriptomic profiling with cDNA microarrays. The 13 C flux analysis revealed that the absolute flux through the oxidative pentose phosphate pathway (oxPPP) was substantially lower (~threefold) under low-nitrogen conditions. Additionally, the flux partitioning ratio between the tricarboxylic acid cycle and anaplerotic pathways varied from 84%:16% under abundant carbon and nitrogen to 55%:45% under deficient carbon and nitrogen. Gene expression data, together with the flux results, suggested a plastidic localization of the oxPPP as well as transcriptional regulation of certain metabolic branchpoints, including those between glycolysis and the oxPPP. The transcriptome data also indicated that NUE-improving mechanisms may involve a redirection of excess carbon to aromatic metabolic pathways and extensive downregulation of potentially redundant genes (in these heterotrophic cells) that encode photosynthetic and light-harvesting proteins, suggesting the recruitment of these proteins as nitrogen sinks in nitrogen-abundant conditions.
Anxiety among informal hospice caregivers: An exploratory study

Abstract Objective: This study examined the prevalence of clinically significant anxiety among informal hospice caregivers and identified the characteristics of caregivers who experienced anxiety of this severity. Method: An exploratory secondary data analysis pooled from three separate studies of informal hospice caregivers (N = 433) was conducted. Researchers employed descriptive statistics to calculate anxiety prevalence and utilized logistic regression to model the associations between the covariates (i.e., caregiver characteristics) and anxiety. Results: Overall, 31% of informal hospice caregivers reported moderate or higher levels of anxiety. Caregivers associated with the research site in the Northwest were less likely to be anxious than those in the Southeast [χ2(3, N = 433) = 7.07, p = 0.029], and employed caregivers were less likely to be anxious than unemployed caregivers (OR = 0.56, 95% CI = 0.33, 0.96). The likelihood of being anxious decreased with increasing physical quality of life (OR = 0.77, 95% CI = 0.69, 0.85), and younger female caregivers were more likely to be anxious than male caregivers and older females (OR = 0.95, CI = 0.91, 0.99). Significance of Results: A noteworthy number of informal hospice caregivers experience clinically significant levels of anxiety. Increased efforts to screen and address anxiety in this population are recommended.
Comparing Symbiotic Efficiency between Swollen versus Nonswollen Rhizobial Bacteroids1[C][W][OA]

Symbiotic rhizobia differentiate physiologically and morphologically into nitrogen-fixing bacteroids inside legume host nodules. The differentiation is apparently terminal in some legume species, such as peas (Pisum sativum) and peanuts (Arachis hypogaea), likely due to extreme cell swelling induced by the host. In other legume species, such as beans (Phaseolus vulgaris) and cowpeas (Vigna unguiculata), differentiation into bacteroids, which are similar in size and shape to free-living rhizobia, is reversible. Bacteroid modification by plants may affect the effectiveness of the symbiosis. Here, we compare symbiotic efficiency of rhizobia in two different hosts where the rhizobia differentiate into swollen nonreproductive bacteroids in one host and remain nonswollen and reproductive in the other. Two such dual-host strains were tested: Rhizobium leguminosarum A34 in peas and beans and Bradyrhizobium sp. 32H1 in peanuts and cowpeas. In both comparisons, swollen bacteroids conferred more net host benefit by two measures: return on nodule construction cost (plant growth per gram nodule growth) and nitrogen fixation efficiency (H2 production by nitrogenase per CO2 respired). Terminal bacteroid differentiation among legume species has evolved independently multiple times, perhaps due to the increased host fitness benefits observed in this study.
IFN-γ action in the media of the great elastic arteries, a novel immunoprivileged site

Infection of medial smooth muscle cells with γ-herpesvirus 68 (γHV68) causes severe chronic vasculitis that is restricted to the great elastic arteries. We show here that persistence of disease in the great elastic arteries is (a) due to inefficient clearance of viral infection from this site compared with other organs or other vascular sites, and (b) associated with failure of T cells and macrophages to enter the virus-infected elastic media. These findings demonstrate immunoprivilege of the media of the great elastic arteries. We found that IFN-γ acted on somatic cells during acute infection to prevent the establishment of medial infection and on hematopoietic cells to determine the severity of disease in this site. The immunoprivileged elastic media may provide a site for persistence of pathogens or self antigens leading to chronic vascular disease, a process regulated by IFN-γ actions on both somatic and hematopoietic cells. These concepts have significant implications for understanding immune responses contributing to or controlling chronic inflammatory diseases of the great vessels.
Time of Day Effects on Repeated Sprint Ability

Abstract The present study aimed at investigating the effects of time-of-day on muscle power and associated electromyographic (EMG) activity level of 4 thigh muscles during a repeated pedalling sprint exercise. After a familiarization session, 12 male subjects were asked to perform the repeated sprint ability test during 2 experimental sessions (randomized order), which were set up either at 06:00 or 18:00 h. For each sprint, peak power output, percentage of peak power decrement and total work were calculated. EMG activity of vastus lateralis, rectus femoris, vastus medialis and biceps femoris muscles was recorded throughout the test and analyzed for each sprint. Total work and percentage of peak power decrement were higher in the evening than in the morning (p<0.01 and p<0.05, respectively). Likewise, peak power was significantly higher at 18:00 than 06:00 h during the first 3 sprints (p<0.01 for sprint 1 and p<0.05 for sprint 2 and 3). There was no time-of-day effect for EMG activity level. The neuromuscular efficiency decreased significantly over the repeated sprint ability test at the 2 times of testing (p<0.01). Despite diurnal fluctuation in muscular power and neuromuscular fatigue during the repeated sprint ability test, EMG activity of major thigh muscles was not time-of-day dependent.