Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasticity of Phymatotrichopsis omnivora infection strategies is dependent on host and nonhost plant responses

Abstract Necrotrophic fungi constitute the largest group of plant fungal pathogens that cause heavy crop losses worldwide. Phymatotrichopsis omnivora is a broad host, soil‐borne necrotrophic fungal pathogen that infects over 2,000 dicotyledonous plants. The molecular basis of such broad host range is unknown. We conducted cell biology and transcriptomic studies in Medicago truncatula (susceptible), Brachypodium distachyon (resistant/nonhost), and Arabidopsis thaliana (partially resistant) to understand P. omnivora virulence mechanisms. We performed defence gene analysis, gene enrichments, and correlational network studies during key infection stages. We identified that P. omnivora infects the susceptible plant as a traditional necrotroph. However, it infects the partially resistant plant as a hemi‐biotroph triggering salicylic acid‐mediated defence pathways in the plant. Further, the infection strategy in partially resistant plants is determined by the host responses during early infection stages. Mutant analyses in A. thaliana established the role of small peptides PEP1 and PEP2 in defence against P. omnivora. The resistant/nonhost B. distachyon triggered stress responses involving sugars and aromatic acids. Bdwat1 mutant analysis identified the role of cell walls in defence. This is the first report that describes the plasticity in infection strategies of P. omnivora providing insights into broad host range.
The association of preoperative anxiety and depression with neurocognitive disorder following oncological surgery

The proposed underlying mechanisms of anxiety and depression, and of postoperative neurocognitive disorder (NCD), each include immune system involvement. Therefore, the aims of this study were to investigate the incidence of postoperative NCD 3 months after surgery among oncological patients undergoing surgery and to evaluate the role of preoperative anxiety and depression.
Cooperativity between Stenotrophomonas maltophilia and Pseudomonas aeruginosa during Polymicrobial Airway Infections

Stenotrophomonas maltophilia is a Gram-negative bacterium found ubiquitously in the environment that has historically been regarded as nonpathogenic. S. maltophilia is increasingly observed in patient sputa in cystic fibrosis (CF), and while existing epidemiology indicates that patients with S. maltophilia have poorer diagnoses, its clinical significance remains unclear. Moreover, as multidrug resistance is common among S. maltophilia isolates, treatment options for these infections may be limited. ABSTRACT Stenotrophomonas maltophilia is a Gram-negative bacterium found ubiquitously in the environment that has historically been regarded as nonpathogenic. S. maltophilia is increasingly observed in patient sputa in cystic fibrosis (CF), and while existing epidemiology indicates that patients with S. maltophilia have poorer diagnoses, its clinical significance remains unclear. Moreover, as multidrug resistance is common among S. maltophilia isolates, treatment options for these infections may be limited. Here, we investigated the pathogenicity of S. maltophilia alone and during polymicrobial infection with Pseudomonas aeruginosa. Colonization, persistence, and virulence of S. maltophilia were assessed in experimental respiratory infections of mice. The results of this study indicate that S. maltophilia transiently colonizes the lung accompanied by significant weight loss and immune cell infiltration and the expression of early inflammatory markers, including interleukin 6 (IL-6), IL-1α, and tumor necrosis factor alpha (TNF-α). Importantly, polymicrobial infection with P. aeruginosa elicited significantly higher S. maltophilia counts in bronchoalveolar lavages and lung tissue homogenates. This increase in bacterial load was directly correlated with the density of the P. aeruginosa population and required viable P. aeruginosa bacteria. Microscopic analysis of biofilms formed in vitro revealed that S. maltophilia formed well-integrated biofilms with P. aeruginosa, and these organisms colocalize in the lung during dual-species infection. Based on these results, we conclude that active cellular processes by P. aeruginosa afford a significant benefit to S. maltophilia during polymicrobial infections. Furthermore, these results indicate that S. maltophilia may have clinical significance in respiratory infections.
Ankyrin-G mediates targeting of both Na+ and KATP channels to the rat cardiac intercalated disc

We investigated targeting mechanisms of Na+ and KATP channels to the intercalated disk (ICD) of cardiomyocytes. Patch clamp and surface biotinylation data show reciprocal downregulation of each other’s surface density. Mutagenesis of the Kir6.2 ankyrin binding site disrupts this functional coupling. Duplex patch clamping and Angle SICM recordings show that INa and IKATP functionally co-localize at the rat ICD, but not at the lateral membrane. Quantitative STORM imaging show that Na+ and KATP channels are localized close to each other and to AnkG, but not to AnkB, at the ICD. Peptides corresponding to Nav1.5 and Kir6.2 ankyrin binding sites dysregulate targeting of both Na+ and KATP channels to the ICD, but not to lateral membranes. Finally, a clinically relevant gene variant that disrupts KATP channel trafficking also regulates Na+ channel surface expression. The functional coupling between these two channels need to be considered when assessing clinical variants and therapeutics.
Delay Maturation in Occipital Lobe in Girls With Inattention Subtype of Attention-Deficit Hyperactivity Disorder

Attention-deficit hyperactivity disorder (ADHD) is a common childhood neuropsychiatric disorder. Differences in the presentations of ADHD between boys and girls have been well established. Three subtypes of ADHD exist. In addition to sex difference, different mechanisms may underlie different subtypes. The present study enrolled 30 girls with the inattentive subtype of ADHD and 30 age-matched controls. Low-resolution electromagnetic tomography (LORETA) and instantaneous frequency were used to analyze electroencephalography (EEG) for investigating the brain area and EEG bands involved in girls with inattentive ADHD. We found that the instantaneous frequencies in all EEG channels in girls with ADHD were lower than those in controls. Alpha 2 was the only EEG band that showed significant difference in current density between the ADHD and control groups (P = .0014). In the entire brain area, the posterior cingulate cortex, cingulate gyrus, and precuneus demonstrated the most significant difference between the ADHD and control groups. Our results suggest that brain maturation delay in the posterior areas might result in the inattention subtype of ADHD. In addition, posterior cingulate cortex, cingulate gyrus, and precuneus may play a critical role in the pathogenesis of ADHD. Our study provides a new approach method and possible mechanism of girls with inattentive subtype ADHD.
Within-family patterns of intergenerational emotional closeness and psychological well-being of older parents in China

Abstract Objectives: There may be a substantial difference in the intergenerational emotional closeness among offspring in a multi-child family, both regarding the overall level as well as the extent to which older parents differentiate emotional closeness between their children. This study addressed different within-family patterns based on the average level and differentiation of older parent–child emotional closeness. It also examined the associations between these distinct patterns and the psychological well-being of older parents in China. Method: We derived a final sample of 4247 older parents (aged 60+) with 14,461 children from the baseline wave (2010) of the China Family Panel Studies. A latent profile analysis was applied to classify within-family patterns based on two indicators: within-family mean level and differentiation of parent–child emotional closeness among offspring. Ordered logistic regression and ordinary least square (OLS) regression were used to investigate the associations between these patterns and older adults’ life satisfaction and depression, respectively. Results: Two family patterns of parent–child emotional closeness were identified: tight-knit (91.50%) and highly ambivalent (8.50%). Compared with the former, older parents having highly ambivalent relationships across multiple offspring tended to have lower life satisfaction and higher levels of depression. Conclusion: This study highlighted the importance of capturing different within-family dynamics of intergenerational emotional closeness in Chinese families. It also pointed out the negative effects of collective ambivalence for older adults’ psychological well-being.
AlpsNMR: an R package for signal processing of fully untargeted NMR-based metabolomics

RESULTS NMR-based metabolomics is widely used to obtain metabolic fingerprints of biological systems. While targeted workflows require previous knowledge of metabolites, prior to statistical analysis, untargeted approaches remain a challenge. Computational tools dealing with fully untargeted NMR-based metabolomics are still scarce or not user-friendly. Therefore, we developed AlpsNMR (Automated spectraL Processing System for NMR), an R package that provides automated and efficient signal processing for untargeted NMR metabolomics. AlpsNMR includes spectra loading, metadata handling, automated outlier detection, spectra alignment and peak-picking, integration, and normalization. The resulting output can be used for further statistical analysis. AlpsNMR proved effective in detecting metabolite changes in a test case. The tool allows less experienced users to easily implement this workflow from spectra to a ready-to-use dataset in their routines. AVAILABILITY The AlpsNMR R package and tutorial is freely available to download from http://github.com/sipss/AlpsNMR under the MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m6A from 3’ untranslated regions is associated with decreased relative transcript abundance and defective RNA 3′ end formation. A functional consequence of disrupted m6A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of what their genomes encode.
Lipid vesicles and nanoparticle for non-invasive topical and transdermal drug delivery.

The delivery of drugs, via different layers of a skin, is challenging because it acts as a natural barrier and exerts hindrance against molecules to permeate into or through it. To overcome such obstacles, different non-invasive methods, like vehicle-drug interaction, modifications of the horny layer and nanoparticles have been suggested. The aim of the present review is to highlight some of the non-invasive methods for topical, diadermal and transdermal delivery of drugs. Special emphasis has been made on the information available in numerous research articles that put efforts in overcoming obstacles associated with barrier functions imparted by various layers of skin. Advances have been made in improving patient compliance that tends to avoid hitches involved in oral administration. Of particular interest is the use of lipid-based vesicles and nanoparticles for dermatological applications. These particulate systems can effectively interact and penetrate into the stratum corneum via lipid exchange and get distributed in epidermis and dermis. They also have the tendency to exert a systemic effect by facilitating the absorption of an active moiety into general circulation.
Evaluation of atrial electromechanical properties in patients with masked hypertension

ABSTRACT Purpose In this study, we evaluated the electromechanical properties of atriums in patients with masked hypertension by using tissue Doppler echocardiographic technique to predict the predisposition to atrial arrhythmias. Methods A total of 118 subjects were included in the study. Twenty-four-hour blood pressure monitorization (ABPM) was used to determinate the masked hypertension in the study group. Tissue Doppler imaging was used to find intra-left and -right atrial electromechanical delay (AEMD) and inter-atrial electromechanical delay. The results compared between patients with masked hypertension and without. Results There were 55 (%46.6) patients with masked hypertension and 63 (%53.4) patients without masked hypertension without any difference regarding age sex heart rate. No statistically significant difference was found in intra-right AEMD between the groups. Left ventricular end-diastolic and systolic diameters (p <0.01 vs p=0.034), left ventricular posterior and septal wall thickness (p < .01 vs p < .01), left ventricular mass index (p <0.01), left atrium volume (p = 0.02), and indexed left atrial volume (p <0 .01) were high in patients with masked hypertension Inter-AEMD (48.07 ± 11.49 ms vs 43.73 ± 8.61 p=0.02) and intra-left AEMD (24.8 ± 6.35 ms vs 21.42 ± 7.99 ms p=0.013) were significantly higher in masked hypertensive patients. Conclusions Masked hypertension shares the same clinical outcomes like overt hypertension. Any effort must be given to prevent unwanted events in masked hypertensive patients. According to our findings we suggesting that masked hypertensive patients must be evaluated for atrial arrhythmia.
Expression of the CCCH‐tandem zinc finger protein gene OsTZF5 under a stress‐inducible promoter mitigates the effect of drought stress on rice grain yield under field conditions

Summary Increasing drought resistance without sacrificing grain yield remains an ongoing challenge in crop improvement. In this study, we report that Oryza sativa CCCH‐tandem zinc finger protein 5 (OsTZF5) can confer drought resistance and increase grain yield in transgenic rice plants. Expression of OsTZF5 was induced by abscisic acid, dehydration and cold stress. Upon stress, OsTZF5‐GFP localized to the cytoplasm and cytoplasmic foci. Transgenic rice plants overexpressing OsTZF5 under the constitutive maize ubiquitin promoter exhibited improved survival under drought but also growth retardation. By introducing OsTZF5 behind the stress‐responsive OsNAC6 promoter in two commercial upland cultivars, Curinga and NERICA4, we obtained transgenic plants that showed no growth retardation. Moreover, these plants exhibited significantly increased grain yield compared to non‐transgenic cultivars in different confined field drought environments. Physiological analysis indicated that OsTZF5 promoted both drought tolerance and drought avoidance. Collectively, our results provide strong evidence that OsTZF5 is a useful biotechnological tool to minimize yield losses in rice grown under drought conditions.
Cadmium-Induced Renal Cell Toxicity Is Associated With MicroRNA Deregulation

Cadmium is an environmental pollutant well known for its nephrotoxic effects. Nevertheless, mechanisms underlying nephrotoxicity continue to be elucidated. MicroRNAs (miRNAs) have emerged in recent years as modulators of xenobiotic-induced toxicity. In this context, our study aimed at elucidating whether miRNAs are involved in renal proximal tubular toxicity induced by cadmium exposure. We showed that cadmium exposure, in 2 distinct renal proximal tubular cell models (renal proximal tubular epithelial cell [RPTEC]/human telomerase reverse transcriptase [hTERT] and human kidney-2), resulted in cytotoxicity associated with morphological changes, overexpression of renal injury markers, and induction of apoptosis and inflammation processes. Cadmium exposure also resulted in miRNA modulation, including the significant upregulation of 38 miRNAs in RPTEC/hTERT cells. Most of these miRNAs are known to target genes whose coding proteins are involved in oxidative stress, inflammation, and apoptosis, leading to tissue remodeling. In conclusion, this study provides a list of dysregulated miRNAs which may play a role in the pathophysiology of cadmium-induced kidney damages and highlights promising cadmium molecular biomarkers that warrants to be further evaluated.
Nanopumping of water via rotation of graphene nanoribbons

In this paper, we perform molecular dynamics simulations to propose a novel bio-inspired nanopumping mechanism that is achieved through the rotation of graphene nanoribbons. Due to the rotation and interaction with water, the graphene nanoribbons undergo morphological transformation. It is shown that with appropriate geometrical and spatial parameters, the resulting morphology is twisted ribbon, which is efficient in pumping of water through a channel. This mimics the propulsive behavior of bacterial flagella through continual rotation at the base and causing morphology of the geometry into twisted ribbons, thus driving flow. It was observed that the maximum flux rate decreases upon reaching the optimal configuration even with increasing rotational speed and graphene width. This is due to the development of cavitation near the region of the nanoribbon with tip velocities approaching the speed of sound in water. The simulation shows promising results where the flux rate of the driven flow outperforms various nanopump configurations that have been reported in recent literature by more than one order.
Characterization of dermal skin innervation in fibromyalgia syndrome

Introduction We characterized dermal innervation in patients with fibromyalgia syndrome (FMS) as potential contribution to small fiber pathology. Methods Skin biopsies of the calf were collected (86 FMS patients, 35 healthy controls). Skin was immunoreacted with antibodies against protein gene product 9.5, calcitonine gene-related peptide, substance P, CD31, and neurofilament 200 for small fiber subtypes. We assessed two skin sections per patient; on each skin section, two dermal areas (150 x 700 μm each) were investigated for dermal nerve fiber length (DNFL). Results In FMS patients we found reduced DNFL of fibers with vessel contact compared to healthy controls (p<0.05). There were no differences for the other nerve fiber subtypes. Discussion We found less dermal nerve fibers in contact with blood vessels in FMS patients than in controls. The pathophysiological relevance of this finding is unclear, but we suggest the possibility of a relationship with impaired thermal tolerance commonly reported by FMS patients.
Qualitative analysis of the Meals, Mindfulness, & Moving Forward (M3) lifestyle programme: Cultivating a ‘safe space’ to start on a ‘new path’ for youth with early episode psychosis

The Meals, Mindfulness, & Moving Forward (M3) programme included nutrition education, hands‐on cooking classes, mindfulness meditation practice, physical activities and facilitated group sharing. M3 was designed as a supplement to standard care for youths (age 15‐25 years) with first‐episode psychosis (FEP) who were clients of coordinated specialty care teams. M3's primary aim was feasibility by demonstrating high programme attendance; secondary aims included cardiometabolic measures. Data collection included quantitative and qualitative outcomes. The aim of the qualitative study was to understand participants' and study partners' experiences during the programme and to understand programme elements that were helpful for young people to sustain healthy lifestyle choices 6 weeks post‐programme.
Sublingual analgesia: a promising proposal for the treatment of pain

The effective, safe and timely management of acute pain is critical. Other than the obvious benefit of reduced suffering, the earlier administration of pain treatment is associated with earlier discharge from the Emergency Department (ED) [1], improved post-operative functionality, less development of chronic pain, and a reduced incidence of post-traumatic stress disorder [2]. While oral opioids (PO) are generally recommended over parenteral opioids [3] there are limited alternatives for the noninvasive management of pain. There are times when a patient may need pain treatment more rapidly than can be achieved with oral opioids or require an agent that is not effective when given PO, but when intravenous (IV) access is either not yet available or otherwise not indicated. In these situations, the sublingual route of administration may offer a useful alternative. Titrating opioids is most easily done using the IV route. Placing an IV, however, can be painful, time consuming, and the fail rate for the first attempt is 12–26% in adults [4], and in some situation IV access is limited. While most severely ill patients need an IV, some patients in moderate or severe pain may not otherwise need one or will require an unknown amount to time to get an IV due to situations complicating access. Accessing veins can be difficult in acute settings such as the Emergency Department, especially in patients who are obese, elderly, have burns, or are needle-phobic. Obesity is the number one reason for difficult IV access in the ED. Needle phobia has been reported in 14–38% of patients [5]. Oral medications have a slow onset. The onset of pain relief from oral medications has been described as around 30 minutes [6], but it is highly variable depending on a wide variety of factors. In addition, most of the opioids that are effective for PO administration are associated with active metabolites, which can complicate the treatment of patients due to variable accumulation and elimination. The variation in onset and elimination can complicate the titration of PO medications, limited their safe and effective use in severe pain or in dynamic situations of progressive pain symptoms. In between IV titration and PO opioids, there are limiting options for acute pain treatment. Intramuscular medications are painful, and the onset is unpredictable, especially in patients with perfusions deficits. Nasal administration has been described for a variety of opioids, but the use is limited by wide variations in efficacy. There are, however, some sublingual opioids available for use that is some cases bridge some of the gaps between IV and PO opioid administration.