Miracle-dz/UniFAR-FTUs huggingface dataset:
Unraveling Reticulate Evolution in Opuntia (Cactaceae) From Southern Mexico

The process of hybridization occurs in approximately 40% of vascular plants, and this exchange of genetic material between non-conspecific individuals occurs unequally among plant lineages, being more frequent in certain groups such as Opuntia (Cactaceae). This genus is known for multiple taxonomic controversies due to widespread polyploidy and probable hybrid origin of several of its species. Southern Mexico species of this genus have been poorly studied despite their great diversity in regions such as the Tehuacán-Cuicatlán Valley which contains around 12% of recognized Mexico’s native Opuntia species. In this work, we focus on testing the hybrid status of two putative hybrids from this region, Opuntia tehuacana and Opuntia pilifera, and estimate if hybridization occurs among sampled southern opuntias using two newly identified nuclear intron markers to construct phylogenetic networks with HyDe and Dsuite and perform invariant analysis under the coalescent model with HyDe and Dsuite. For the test of hybrid origin in O. tehuacana, our results could not recover hybridization as proposed in the literature, but we found introgression into O. tehuacana individuals involving O. decumbens and O. huajuapensis. Regarding O. pilifera, we identified O. decumbens as probable parental species, supported by our analysis, which sustains the previous hybridization hypothesis between Nopalea and Basilares clades. Finally, we suggest new hybridization and introgression cases among southern Mexican species involving O. tehuantepecana and O. depressa as parental species of O. velutina and O. decumbens.
O-aryl and Carbonyl Carbon Contents of Food Waste and Biosolid Predict P Availability in an Acidic Soil

Organic waste streams, otherwise known as organic amendments (OA), contain potentially valuable nutrients which may additionally increase legacy nutrient availability in soil. This is particularly the case for phosphorus (P) where declining reserves of rock phosphate add an extra dimension to their utility. In acidic soils, OA have been reported to increase P availability through the action of O-aryl and carbonyl groups (represent organic acid compounds) by substituting previously fixed, legacy P and forming organometallic complexes to reduce P sorption. This study aimed to investigate if signature P (orthophosphate) and C (O-aryl and carbonyl) content of OA could be used to predict soil P availability, to replace traditional ways of testing OA and also for future prescriptive applications. Food waste and biosolid were the sources of OA in this study, with pyrolysis and composting processes used to create a range of functional groups. Nuclear magnetic resonance (NMR) spectroscopy was utilized to identify forms of C (solid-state 13C NMR) and P compounds (solution-state 31P NMR) in these OA. The O-aryl, carbonyl, and orthophosphate content were higher in pyrolysis and composted materials compared to their feedstock substrate. The effect of OA addition on soil P availability was monitored in a 110-day laboratory incubation study. Results showed an increase in soil P availability (Olsen P) and a decrease in soil P buffering capacity (PBC) after incubation. The increase in soil P availability was not predicted well by the NMR-derived orthophosphate content of OA, which may be due to the overestimation of plant-available orthophosphate content by the solution-state 31P NMR. Furthermore, an additional increase in soil ΔOlsen P (difference between observed and expected) was obtained above the Olsen P added from OA indicating substitution of previously fixed soil P. Both indices of P availability namely ΔOlsen P (r = 0.63–0.83) and ΔPBC (difference between treatment—control) (r = −0.50 to −0.80) showed strong (but opposite) correlations with the ratio of O-aryl to carbonyl C content of OA. It was concluded that the ratio of O-aryl and carbonyl C content of OA could be used to predict the P availability in acidic soil.
Montelukast Use Decreases Cardiovascular Events in Asthmatics

Cysteinyl leukotrienes are proinflammatory mediators with a clinically established role in asthma and a human genetic and preclinical role in cardiovascular pathology. Given that cardiovascular disease has a critical inflammatory component, the aim of this work was to conduct an observational study to verify whether the use of a cysteinyl leukotriene antagonist, namely, montelukast, may protect asthmatic patients from a major cardiovascular event and, therefore, represent an innovative adjunct therapy to target an inflammatory component in cardiovascular disease. We performed an observational retrospective 3-year study on eight hundred adult asthmatic patients 18 years or older in Albania, equally distributed into two cohorts, exposed or nonexposed to montelukast usage, matched by age and gender according to information reported in the data collection. Patients with a previous history of myocardial infarction or ischemic stroke were excluded. In summary, 37 (4.6%) of the asthmatic patients, 32 nonexposed, and five exposed to montelukast suffered a major cardiovascular event during the 3-year observation period. All the cardiovascular events, in either group, occurred among patients with an increased cardiovascular risk. Our analyses demonstrate that, independent from gender, exposure to montelukast remained a significant protective factor for incident ischemic events (78% or 76% risk reduction depending on type of analysis). The event-free Kaplan–Meier survival curves confirmed the lower cardiovascular event incidence in patients exposed to montelukast. Our data suggest that there is a potential preventative role of montelukast for incident cardiac ischemic events in the older asthmatic population, indicating a comorbidity benefit of montelukast usage in asthmatics by targeting cysteinyl leukotriene-driven cardiac disease inflammation.
Relevance of Neonatal Behavior Assessment Scale for Infants With Somatic Disorders: Comparison on One Matched Group of Control

Objective: To compare the Neonatal Behavior Assessment Scale results in two groups of infants with or without somatic disorder (N = 26). Method: The Neonatal Behavior Assessment Scale was administered to two groups (clinical and control) of 13 infants each, aged from 5 to 18 weeks, matched 2 by 2 according to sex, age, rank among siblings, and parental socio-professional category. The first group includes infants with somatic disorder (clinical) and is matched with a second group of “healthy infants” (control). Results: Results indicate that the mean score of the control group is significantly higher than that of the clinical group. Most of the items are affected by the presence of a somatic disorder. Indeed, five out of the six categories present a statistically significant difference in favor of the control group, more specifically for the items “state regulation,” “motor system,” and “orientation/interaction. ” Conclusion: This exploratory research enables a precise description of infants' difficulty in regulating excitations and the impact of somatic disorders on their development. This innovative knowledge will assist pediatricians and health professionals in the understanding of infants' characteristics to develop an adapted-care.
Dissecting the Genotypic Variation of Growth Responses to Far-Red Radiation in Tomato

The recent development of light-emitting diodes (LEDs) and their application in modern horticulture stimulated studies demonstrating that additional far-red (FR) radiation (700–800 nm) increases plant dry mass. This effect of FR has been explained by improved photosynthesis and/or plant architecture. However, the genotypic variation in this response is largely unknown. Here, we aim to explore and explain the genotypic variation in growth responses to additional FR. We expected the genotypic variation in the responses of plant dry mass to additional FR. Further, we hypothesized that a significant improvement of both net assimilation rate (NAR) and leaf area ratio (LAR) is responsible for a strong dry mass increase under additional FR, while some genotypes respond only marginally or even negatively in NAR or LAR under FR, thus resulting in a weak FR effect on plant dry mass. To test these hypotheses, we grew 33 different tomato genotypes for 21 days with 0, 25, or 100 μmol m–2 s–1 of FR added to a common white + red LED background lighting of 150 μmol m–2 s–1. Genotypes responded similarly with respect to plant height, stem dry mass, and shoot:root ratio; i.e., they all increased with increasing FR. However, the response of total plant dry mass varied among genotypes. We categorized the genotypes into three groups (strongly, moderately, and weakly responding groups) based on their relative response in total plant dry mass to FR. Growth component analysis revealed that the strongly responding genotypes increased strongly in NAR rather than LAR. The weakly responding genotypes, however, showed a substantial increase in LAR but not NAR. The increase in LAR was due to the increase in specific leaf area. Leaf mass fraction, which is the other component of LAR, decreased with FR and did not differ between groups. In conclusion, tomato genotypes that increased strongly in NAR in response to FR were able to achieve a more substantial increase in dry mass than did other genotypes. This is the first study to explain the differences in growth responses of a large number of tomato genotypes toward FR in their light environment.
Neoadjuvant EGFR-TKI Therapy for EGFR-Mutant NSCLC: A Systematic Review and Pooled Analysis of Five Prospective Clinical Trials

Purpose The role of neoadjuvant epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI) targeted therapy for patients with EGFR-mutant non-small cell lung cancer (NSCLC) has not been clarified. A pooled analysis of prospective clinical trials was conducted to evaluate the efficacy and safety of neoadjuvant EGFR-TKI therapy. Methods The PubMed, Embase, Web of Science, and Cochrane Library databases, as well as meeting abstracts were searched for prospective clinical trials evaluating the efficacy and safety of neoadjuvant EGFR-TKI for treatment of EGFR-mutant NSCLC. The main outcomes included the objective response rate (ORR), downstaging rate, surgical resection rate (SRR), pathologic complete response (pCR) rate, progression-free survival (PFS), and adverse events. Results A total of five, phase II, prospective, clinical trials involving 124 patients with resectable or potentially resectable EGFR-mutant NSCLC treated with neoadjuvant erlotinib or gefitinib treatment were included in this pooled analysis. The median neoadjuvant medication time was 42 (range, 21–56) days and the median time of response evaluation was 45 (range, 42–56) days. The pooled ORR was 58.5% [95% confidence interval (CI), 45.5%–71.8%] and the surgical resection and complete resection (R0) rates were 79.9% (95% CI, 65.3%–94.5%) and 64.3% (95% CI, 43.8%–84.8%), respectively. In the stage IIIA subgroup (n = 68), the pooled ORR, SRR, and R0 rate were 51.4%, 72.9%, and 57.0%, respectively, while the downstaging and pCR rates were 14.0% and 0.0%, respectively. The pooled median PFS and overall survival were 13.2 and 41.9 months, respectively. Of the most common grade 3/4 adverse events in the overall group, the incidences of hepatotoxicity and skin rash were 5.3% and 14.7%, respectively. The most commonly reported postoperative complications were lung infection, arrhythmia, and pneumothorax. Conclusion Neoadjuvant EGFR-TKI therapy provides a feasible treatment modality for patients with resectable or potentially resectable EGFR-mutant NSCLC, with satisfactory surgical outcomes and low toxicity. Although further phase III clinical trials are needed to confirm these findings, it is necessary to explore the feasibility of a more effective EGFR-TKI combination neoadjuvant therapy given the modest downgrade and pCR rates for EGFR-TKI alone.
CPEB4-Promoted Paclitaxel Resistance in Ovarian Cancer In Vitro Relies on Translational Regulation of CSAG2

Background: Drug resistance is a major obstacle in chemotherapy for ovarian cancer, wherein the up regulation of drug-resistant genes plays an important role. The cytoplasmic polyadenylation element binding protein 4 (CPEB4) is an RNA binding protein that controls mRNA cytoplasmic polyadenylation and translation. Methods: The expression of CPEB4 in paclitaxel-resistant ovarian cancer cell lines and recurrent ovarian tumors relative to counterparts was determined by qRT-PCR, Western blotting and immunohistochemistry. The response to paclitaxel treatment was evaluated by cellular viability test and colony formation assay. RNA immunoprecipitation and poly(A) tail test were applied to examine the levels of RNA binding and cytoplasmic polyadenylation. Results: CPEB4 is elevated in paclitaxel-resistant ovarian cancer cells and recurrent ovarian tumors treated with paclitaxel-based chemotherapy. In addition, CPEB4 overexpression promotes paclitaxel resistance in ovarian cancer cells in vitro, and vice versa, CPEB4 knockdown restores paclitaxel sensitivity, indicating that CPEB4 confers paclitaxel resistance in ovarian cancer cells. Mechanistically, CPEB4 binds with the taxol (paclitaxel)-resistance-associated gene-3 (TRAG-3/CSAG2) mRNAs and induces its expression at a translational level. Moreover, CSAG2 expression is upregulated in paclitaxel-resistant ovarian carcinoma and cancer cell lines, and more importantly, siRNA-mediated CSAG2 knockdown overtly attenuates CPEB4-mediated paclitaxel resistance. Conclusion: This study suggests that the drug-resistant protein CSAG2 is translationally induced by CPEB4, which underlies CPEB4-promoted paclitaxel resistance in ovarian cancer in vitro. Thus, interfering CPEB4/CSAG2 axis might be of benefit to overcome paclitaxel-resistant ovarian cancer.
Histology and RNA Sequencing Provide Insights Into Fusarium Head Blight Resistance in AAC Tenacious

Fusarium head blight (FHB) is a serious fungal disease affecting wheat and other cereals worldwide. This fungus causes severe yield and quality losses from a reduction in grain quality and contamination of grain with mycotoxins. Intensive breeding efforts led to the release of AAC Tenacious, which was the first spring wheat cultivar registered in Canada with a resistant (R) rating to FHB. To elucidate the physiological mechanisms of resistance, we performed histological and transcriptomic analyses of AAC Tenacious and a susceptible control Roblin after inoculation with Fusarium graminearum (Fg). The spikelet and rachis of infected wheat spikes were hand sectioned and monitored by confocal and fluorescent microscopy. Visible hyphae were observed within the inoculated spikelets for AAC Tenacious; however, the infection was largely restricted to the point of inoculation (POI), whereas the adjacent florets in Roblin were heavily infected. Significant cell wall thickening within the rachis node below the POI was evident in AAC Tenacious compared to Roblin in response to Fg inoculation. Rachis node and rachilla tissues from the POI and the rachis node below the POI were collected at 5 days post inoculation for RNAseq. Significant changes in gene expression were detected in both cultivars in response to infection. The rachis node below the POI in AAC Tenacious had fewer differentially expressed genes (DEGs) when compared to the uninoculated control, likely due to its increased disease resistance. Analysis of DEGs in Roblin and AAC Tenacious revealed the activation of genes and pathways in response to infection, including those putatively involved in cell wall modification and defense response.
The Neuroimmunology of Guillain-Barré Syndrome and the Potential Role of an Aging Immune System

Guillain-Barré syndrome (GBS) is a paralyzing autoimmune condition affecting the peripheral nervous system (PNS). Within GBS there are several variants affecting different aspects of the peripheral nerve. In general, there appears to be a role for T cells, macrophages, B cells, and complement in initiating and perpetuating attacks on gangliosides of Schwann cells and axons. Of note, GBS has an increased prevalence and severity with increasing age. In addition, there are alterations in immune cell functioning that may play a role in differences in GBS with age alongside general age-related declines in reparative processes (e.g., delayed de-differentiation of Schwann cells and decline in phagocytic ability of macrophages). The present review will explore the immune response in GBS as well as in animal models of several variants of the disorder. In addition, the potential involvement of an aging immune system in contributing to the increased prevalence and severity of GBS with age will be theorized.
Interactions Between Allogeneic Mesenchymal Stromal Cells and the Recipient Immune System: A Comparative Review With Relevance to Equine Outcomes

Despite significant immunosuppressive activity, allogeneic mesenchymal stromal cells (MSCs) carry an inherent risk of immune rejection when transferred into a recipient. In naïve recipients, this immune response is initially driven by the innate immune system, an immediate reaction to the foreign cells, and later, the adaptive immune system, a delayed response that causes cell death due to recognition of specific alloantigens by host cells and antibodies. This review describes the actions of MSCs to both suppress and activate the different arms of the immune system. We then review the survival and effectiveness of the currently used allogeneic MSC treatments.
Using Genetic Engineering Techniques to Develop Banana Cultivars With Fusarium Wilt Resistance and Ideal Plant Architecture

Bananas (Musa spp.) are an important fruit crop worldwide. The fungus Fusarium oxysporum f. sp. cubense (Foc), which causes Fusarium wilt, is widely regarded as one of the most damaging plant diseases. Fusarium wilt has previously devastated global banana production and continues to do so today. In addition, due to the current use of high-density banana plantations, desirable banana varieties with ideal plant architecture (IPA) possess high lodging resistance, optimum photosynthesis, and efficient water absorption. These properties may help to increase banana production. Genetic engineering is useful for the development of banana varieties with Foc resistance and ideal plant architecture due to the sterility of most cultivars. However, the sustained immune response brought about by genetic engineering is always accompanied by yield reductions. To resolve this problem, we should perform functional genetic studies of the Musa genome, in conjunction with genome editing experiments, to unravel the molecular mechanisms underlying the immune response and the formation of plant architecture in the banana. Further explorations of the genes associated with Foc resistance and ideal architecture might lead to the development of banana varieties with both ideal architecture and pathogen super-resistance. Such varieties will help the banana to remain a staple food worldwide.
Confined Brownian Motion Tracked With Motion Blur: Estimating Diffusion Coefficient and Size of Confining Space

Mesoscopic environments and particles diffusing in them are often studied by tracking such particles individually while their Brownian motion explores their environment. Environments may be, e.g., a domain in a cell membrane, an interior compartment of a cell, or an engineered nanopit. Particle trajectories are typically determined from time-lapse recorded movies. These are recorded with sufficient exposure time per frame to be able to detect and localize particles in each frame. Since particles move during this exposure time, particles image with motion blur. This motion blur can compromise estimates of diffusion coefficients and the size of the confining domain if not accounted for correctly. We do that here. We give explicit and exact expressions for the variance of measured positions and the mean-squared displacement of a Brownian particle confined in, respectively, a 1D box, a 2D box, a 2D circular disc, and a 3D sphere. Our expressions are valid for all exposure times, irrespective of the size of the confining space and the value of the diffusion coefficient. They apply also in the common case where the exposure time is smaller than the time-lapse due, e.g., to “dead time” caused by the readout process in the camera. These expressions permit determination of diffusion coefficients and domain sizes for given movies for the simple geometries we consider. More important, the trends observed in our exact results when parameter values are varied are valid also for more complex geometries for which no exact analytical solutions exist. Wherever the underlying physics is the same, the exact quantitative description of its consequences provided here is portable as a qualitative and semi-quantitative understanding of its consequences in general. The results may also be useful for other types of reflected Brownian motion than those occurring in single-particle tracking, e.g., in nuclear magnetic resonance imaging techniques. For use in that particular context, we briefly discuss the effects of confinement on anisotropic Brownian motion imaged with motion blur.
Induction of the Stringent Response Underlies the Antimicrobial Action of Aliphatic Isothiocyanates

Bacterial resistance to known antibiotics comprises a serious threat to public health. Propagation of multidrug-resistant pathogenic strains is a reason for undertaking a search for new therapeutic strategies, based on newly developed chemical compounds and the agents present in nature. Moreover, antibiotic treatment of infections caused by enterotoxin toxin-bearing strain—enterohemorrhagic Escherichia coli (EHEC) is considered hazardous and controversial due to the possibility of induction of bacteriophage-encoded toxin production by the antibiotic-mediated stress. The important source of potentially beneficial compounds are secondary plant metabolites, isothiocyanates (ITC), and phytoncides from the Brassicaceae family. We reported previously that sulforaphane and phenethyl isothiocyanate, already known for their chemopreventive and anticancer features, exhibit significant antibacterial effects against various pathogenic bacteria. The mechanism of their action is based on the induction of the stringent response and accumulation of its alarmones, the guanosine penta- and tetraphosphate. In this process, the amino acid starvation path is employed via the RelA protein, however, the precise mechanism of amino acid limitation in the presence of ITCs is yet unknown. In this work, we asked whether ITCs could act synergistically with each other to increase the antibacterial effect. A set of aliphatic ITCs, such as iberin, iberverin, alyssin, erucin, sulforaphen, erysolin, and cheirolin was tested in combination with sulforaphane against E. coli. Our experiments show that all tested ITCs exhibit strong antimicrobial effect individually, and this effect involves the stringent response caused by induction of the amino acid starvation. Interestingly, excess of specific amino acids reversed the antimicrobial effects of ITCs, where the common amino acid for all tested compounds was glycine. The synergistic action observed for iberin, iberverin, and alyssin also led to accumulation of (p)ppGpp, and the minimal inhibitory concentration necessary for the antibacterial effect was four- to eightfold lower than for individual ITCs. Moreover, the unique mode of ITC action is responsible for inhibition of prophage induction and toxin production, in addition to growth inhibition of EHEC strains. Thus, the antimicrobial effect of plant secondary metabolites by the stringent response induction could be employed in potential therapeutic strategies.