Miracle-dz/UniFAR-FTUs huggingface dataset:
Anther Culture Efficiency in Quality Hybrid Rice: A Comparison between Hybrid Rice and Its Ratooned Plants

An immense increase in human population along with diminished lands necessitates the increase of rice production since, it serves the human population as a staple food. Though rice hybrids (RH) are showing considerable yield enhancement over inbreds in terms of both quality and quantity, farmers’ adoption of hybrid rice technology has been much slower than expected because of several constraints such as seed cost and quality. Doubled haploid (DH) technology was considered useful for the development of inbred lines from rice hybrids in a single generation. Androgenesis shows its significance in development of DHs in rice which requires an efficient method to establish the production of large population. To start the anther culture, anthers are the main component of androgenesis to be isolated from unopened spikes. However, the duration of spikes availability for anther culture coupled with the segregation of rice hybrids in the next generation requires the main crop be ratooned to reduce the cost of cultivation. Therefore, the efficiency of the androgenic method was tested in main crop using a quality indica rice hybrid, 27P63 and its ratooned ones. The effects of various factors such as cold temperature pre-treatment of boots, treatment duration, and different combination of plant growth regulators (PGR) on callus response along with shoot regeneration were tested for development of DHs from both ratooned and non-ratooned plants. The N6 medium supplemented with 2.0 mg/L 2,4-D (2,4-dichlrophenoxy acetic acid), 0.5 mg/L BAP (6-benzylamino purine), and 30 g/L maltose was found to be most effective for callusing as compared to MS (Murashige and Skoog) medium. The N6 media inducted calli showed maximum response rate for green shoot regeneration in MS media supplemented with 0.5 mg/L NAA (1-napthaleneacetic acid), 0.5 mg/L Kn (Kinetin; 6-furfurylaminopurine), 1.5 mg/L BAP and 30 g/L sucrose after 2 weeks of culture. The pre-treatment of spikes at 10 °C for 2 d followed by a 7th and 8th d were found to be most effective for callusing as well as for regeneration, producing a total of 343 green plants from ratooned and main rice hybrid, 27P63. Morpho-agronomic trait-based assessment of ploidy status revealed 94.46% diploids, 3.49% polyploids, 0.58% mixploids, and 1.45% haploids. Microsatellite markers could authenticate all 324 fertile diploids as true DHs. Though this study shows a reduction in generation of DHs from ratooned plants as compared to the main crop, manipulation of chemical factors could optimize the method to enhance the production of considerable number of DHs. Utilization of ratooned of hybrid rice in androgenesis would save time and cost of cultivation.
Employing molecularly imprinted polymers in the development of electroanalytical methodologies for antibiotic determination

Antibiotics, although being amazing compounds, need to be monitored in the environment and foodstuff. This is primarily to prevent the development of antibiotic resistance that may make them ineffective. Unsurprisingly, advances in analyticalsciences that can improve their determination are appreciated. Electrochemical techniques are known for their simplicity, sensitivity, portability and low‐cost; however, they are often not selective enough without recurring to a discriminating element like an antibody. Molecular imprinting technology aims to create artificial tissues mimicking antibodies named molecularly imprinted polymers (MIPs), these retain the advantages of selectivity but without the typical disadvantages of biological material, like limited shelf‐life and high cost. This manuscript aims to review all analytical methodologies for antibiotics, using MIPs, where the detection technique is electrochemical, like differential pulse voltammetry (DPV), square‐wave voltammetry (SWV) or electrochemical impedance spectroscopy (EIS). MIPs developed by electropolymerization (e‐MIPs) were applied in about 60 publications and patents found in the bibliographic search, while MIPs developed by other polymerization techniques, like temperature assisted (“bulk”) or photopolymerization, were limited to around 40. Published works covered the electroanalysis of a wide range of different antibiotics (β‐lactams, tetracyclines, quinolones, macrolides, aminoglycosides, among other), in a wide range of matrices (food, environmental and biological).
A Novel Secreted Cysteine-Rich Anionic (Sca) Protein from the Citrus Postharvest Pathogen Penicillium digitatum Enhances Virulence and Modulates the Activity of the Antifungal Protein B (AfpB)

Antifungal proteins (AFPs) from ascomycete fungi could help the development of antimycotics. However, little is known about their biological role or functional interactions with other fungal biomolecules. We previously reported that AfpB from the postharvest pathogen Penicillium digitatum cannot be detected in the parental fungus yet is abundantly produced biotechnologically. While aiming to detect AfpB, we identified a conserved and novel small Secreted Cysteine-rich Anionic (Sca) protein, encoded by the gene PDIG_23520 from P. digitatum CECT 20796. The sca gene is expressed during culture and early during citrus fruit infection. Both null mutant (Δsca) and Sca overproducer (Scaop) strains show no phenotypic differences from the wild type. Sca is not antimicrobial but potentiates P. digitatum growth when added in high amounts and enhances the in vitro antifungal activity of AfpB. The Scaop strain shows increased incidence of infection in citrus fruit, similar to the addition of purified Sca to the wild-type inoculum. Sca compensates and overcomes the protective effect of AfpB and the antifungal protein PeAfpA from the apple pathogen Penicillium expansum in fruit inoculations. Our study shows that Sca is a novel protein that enhances the growth and virulence of its parental fungus and modulates the activity of AFPs.
Performance of Prognostic Scoring Systems in Trauma Patients in the Intensive Care Unit of a Trauma Center

Background: Prediction of mortality outcomes in trauma patients in the intensive care unit (ICU) is important for patient care and quality improvement. We aimed to measure the performance of 11 prognostic scoring systems for predicting mortality outcomes in trauma patients in the ICU. Methods: Prospectively registered data in the Trauma Registry System from 1 January 2016 to 31 December 2018 were used to extract scores from prognostic scoring systems for 1554 trauma patients in the ICU. The following systems were used: the Trauma and Injury Severity Score (TRISS); the Acute Physiology and Chronic Health Evaluation (APACHE II); the Simplified Acute Physiology Score (SAPS II); mortality prediction models (MPM II) at admission, 24, 48, and 72 h; the Multiple Organ Dysfunction Score (MODS); the Sequential Organ Failure Assessment (SOFA); the Logistic Organ Dysfunction Score (LODS); and the Three Days Recalibrated ICU Outcome Score (TRIOS). Predictive performance was determined according to the area under the receiver operator characteristic curve (AUC). Results: MPM II at 24 h had the highest AUC (0.9213), followed by MPM II at 48 h (AUC: 0.9105). MPM II at 24, 48, and 72 h (0.8956) had a significantly higher AUC than the TRISS (AUC: 0.8814), APACHE II (AUC: 0.8923), SAPS II (AUC: 0.9044), MPM II at admission (AUC: 0.9063), MODS (AUC: 0.8179), SOFA (AUC: 0.7073), LODS (AUC: 0.9013), and TRIOS (AUC: 0.8701). There was no significant difference in the predictive performance of MPM II at 24 and 48 h (p = 0.37) or at 72 h (p = 0.10). Conclusions: We compared 11 prognostic scoring systems and demonstrated that MPM II at 24 h had the best predictive performance for 1554 trauma patients in the ICU.
Electronic Medical Record-Based Pager Notification Reduces Excess Oxygen Exposure in Mechanically Ventilated Subjects

BACKGROUND: Liberal oxygenation during mechanical ventilation is harmful in critically ill patients and in certain subsets of patients, including those with stroke, acute myocardial infarction, and cardiac arrest. Surveillance through electronic medical records improves safety of mechanical ventilation in the ICU. To date, this practice has not been used for oxygen titration (FIO2) in adults. We hypothesize that a surveillance system based on the electronic medical record to alert respiratory therapists to titrate FIO2 is feasible, safe, and efficacious. METHODS: In this pilot study, mechanically ventilated subjects were randomized to respiratory therapist-driven FIO2 titration after an electronic alert versus standard of care (ie, titration based on physician order). An automated surveillance system utilizing a hyperoxemia-detection algorithm generated an electronic alert to a respiratory therapist’s pager. Hyperoxemia was defined as FIO2 > 0.5 and SpO2 > 95% for > 30 min. No other aspects of treatment were changed. We assessed feasibility, safety, and preliminary efficacy. Primary outcome was duration of hyperoxemia during mechanical ventilation. An unsafe outcome was identified as hypoxemia (SpO2 < 88%) within 1 h after titration per alert. Feasibility was assessed by a survey of respiratory therapists. RESULTS: Of 226 randomized subjects, 31 were excluded (eg, programming errors of the electronic alerts, no consent, physician discretion). We included 195 subjects, of whom 86 were in the intervention arm. Alert accuracy was 78%, and respiratory therapists responded to 64% of the alerts. During mechanical ventilation, exposure to hyperoxemia significantly decreased in the intervention group (median 13.5 h [interquartile range 6.2–29.4] vs 18.8 h [interquartile range 9.6–37.4]). No episodes of significant hypoxemia were registered. Most respiratory therapists agreed that the alert was helpful in reducing excessive oxygen exposure. CONCLUSIONS: Use of an electronic surveillance system to titrate FIO2 was safe and feasible and showed preliminary efficacy in reducing hyperoxemia. Our study serves to justify larger randomized controlled trials for FIO2 titration.
Development on Citrus medica infected with ‘Candidatus Liberibacter asiaticus’ has sex-specific and -nonspecific impacts on adult Diaphorina citri and its endosymbionts

Huanglongbing (HLB) is a deadly, incurable citrus disease putatively caused by the unculturable bacterium, ‘Candidatus Liberibacter asiaticus’ (CLas), and transmitted by Diaphorina citri. Prior studies suggest D. citri transmits CLas in a circulative and propagative manner; however, the precise interactions necessary for CLas transmission remain unknown, and the impact of insect sex on D. citri-CLas interactions is poorly understood despite reports of sex-dependent susceptibilities to CLas. We analyzed the transcriptome, proteome, metabolome, and microbiome of male and female adult D. citri reared on healthy or CLas-infected Citrus medica to determine shared and sex-specific responses of D. citri and its endosymbionts to CLas exposure. More sex-specific than shared D. citri responses to CLas were observed, despite there being no difference between males and females in CLas density or relative abundance. CLas exposure altered the abundance of proteins involved in immunity and cellular and oxidative stress in a sex-dependent manner. CLas exposure impacted cuticular proteins and enzymes involved in chitin degradation, as well as energy metabolism and abundance of the endosymbiont ‘Candidatus Profftella armatura’ in both sexes similarly. Notably, diaphorin, a toxic Profftella-derived metabolite, was more abundant in both sexes with CLas exposure. The responses reported here resulted from a combination of CLas colonization of D. citri as well as the effect of CLas infection on C. medica. Elucidating these impacts on D. citri and their endosymbionts contributes to our understanding of the HLB pathosystem and identifies the responses potentially critical to limiting or promoting CLas acquisition and propagation in both sexes.
The Oncoprotein SKI Acts as A Suppressor of NK Cell-Mediated Immunosurveillance in PDAC

Simple Summary Pancreatic ductal adeno carcinoma is one of the most lethal solid tumors and the survival rate has not improved significantly over the past decades. The disease is characterized by an immune-suppressive tumor microenvironment, which promotes the limited response to novel immunotherapies. The aim of our study was to contribute to a better understanding of the diminished Natural Killer (NK) cell-activity in pancreatic cancer. We showed that oncoprotein SKI, which is involved in CBP/p300-mediated acetylation, diminished the expression of activating ligands for the cytotoxicity receptor NKG2D on tumor cells, thereby counteracting NK cell-dependent cytotoxicity. Treatment of tumor cells with histone deacetylase inhibitors (HDACi) induced the expression of these ligands and improved NK cell-dependent killing. Thus, we unraveled a so far unknown role of SKI in NK cell-mediated immunosurveillance. Our results suggest that the combination of HDACi with NK cell-based immunotherapies may be beneficial for pancreatic cancer patients. Abstract Drugs targeting epigenetic mechanisms such as histone deacetylase inhibitors (HDACi) suppress tumor growth. HDACi also induce the expression of ligands for the cytotoxicity receptor NKG2D rendering tumors more susceptible to natural killer (NK) cell-dependent killing. The major acetylases responsible for the expression of NKG2D ligands (NKG2D-L) are CBP and p300. The role of the oncogene and transcriptional repressor SKI, an essential part of an HDAC-recruiting co-repressor complex, which competes with CBP/p300 for binding to SMAD3 in TGFβ signaling, is unknown. Here we show that the siRNA-mediated downregulation of SKI in the pancreatic cancer cell lines Panc-1 and Patu8988t leads to an increased target cell killing by primary NK cells. However, the higher cytotoxicity of NK cells did not correlate with the induction of NKG2D-L. Of note, the expression of NKG2D-L and consequently NK cell-dependent killing could be induced upon LBH589 (LBH, panobinostat) or valproic acid (VPA) treatment irrespective of the SKI expression level but was significantly higher in pancreatic cancer cells upon genetic ablation of SKI. These data suggest that SKI represses the inducible expression of NKG2D-L. The combination of HDACi with NK cell-based immunotherapy is an attractive treatment option for pancreatic tumors, specifically for patients with high SKI protein levels.
The changed functional status of the brain was involved in patients with poststroke aphasia: Coordinate‐based (activation likelihood estimation) meta‐analysis

Although many functional magnetic resonance imaging (fMRI) studies have investigated the language architecture and neurobiological mechanism underlying poststroke aphasia (PSA), the pathophysiological mechanisms of PSA still remain poorly understood. In addition to a limited number of subjects (<20) tested with different methodologies and stimuli, inconsistent reports of the brain regions involved have been a major factor. Thus, we conducted a meta‐analysis of 12 peer‐reviewed studies of abnormal brain activation regions in PSA patients at rest using activation likelihood estimation (ALE).
Novel peptide derived from IGF‐2 displays anti‐angiogenic activity in vitro and inhibits retinal angiogenesis in a model of oxygen‐induced retinopathy

Retinopathy of prematurity (ROP), a major cause of significant visual morbidity and blindness in preterm infants, is closely related to pathological angiogenesis. The aim of the study is to evaluate the effect of a new 12‐aa peptide (named peptide CW‐703) from human insulin‐like growth factor‐2, against angiogenesis in ROP.
Metagenome analysis from the sediment of river Ganga and Yamuna: In search of beneficial microbiome

Beneficial microbes are all around us and it remains to be seen, whether all diseases and disorders can be prevented or treated with beneficial microbes. In this study, the presence of various beneficial bacteria were identified from the sediments of Indian major Rivers Ganga and Yamuna from nine different sites using a metagenomic approach. The metagenome sequence analysis using the Kaiju Web server revealed the presence of 69 beneficial bacteria. Phylogenetic analysis among these bacterial species revealed that they were highly diverse. Relative abundance analysis of these bacterial species is highly correlated with different pollution levels among the sampling sites. The PCA analysis revealed that Lactobacillus spp. group of beneficial bacteria are more associated with sediment sampling sites, KAN-2 and ND-3; whereas Bacillus spp. are more associated with sites, FAR-2 and ND-2. This is the first report revealing the richness of beneficial bacteria in the Indian rivers, Ganga and Yamuna. The study might be useful in isolating different important beneficial microorganisms from these river sediments, for possible industrial applications.
Dietary health perceptions and sources of nutritional knowledge in an urban food environment: a qualitative study from Indonesia

Abstract Objective: To investigate dietary health understandings, healthy foods access perceptions and the main sources of nutritional knowledge of residents in three urban communities of varying socio-economic make-up. Design: An ethnographic approach to primary qualitative data collection, involving frequent visits to study areas over 4 months and in-depth interviews. Interviews were recorded, transcribed verbatim and analysed through an iterative approach. Setting: Yogyakarta, Indonesia. Participants: A purposive sample of 45 participants divided equally among the 3 communities. Participants were mostly female (93 %), aged between 27 and 75 years (mean 47·7) and largely identified as the person responsible for household food-related decisions (93 %). Results: Three overarching themes emerged: (i) dietary health understandings; (ii) healthy foods access perceptions and (iii) sources of nutritional knowledge. Participants employed multifaceted conceptualisation of dietary health. Most identified healthy foods with traditional plant-based foods, inexpensive and locally available from multiple sources. Thus, all participants perceived healthy foods as highly available in the local environment and most (80 %) as affordable. Reported affordability issues referred to specific foods (particularly animal source products) and were independent of income levels. Participants acquired nutritional knowledge from multiple sources, including many community-based initiatives. These were overall perceived as useful, but also as presenting some limitations. Conclusions: The variety in dietary health understandings reported by study participants, and their high perceptions of healthy foods availability in the local environment reinforce the idea that individual- and food environment-level determinants of nutritional behaviours are highly contextual.
Toxic Metals (Al, Cd, Pb) and Trace Element (B, Ba, Co, Cu, Cr, Fe, Li, Mn, Mo, Ni, Sr, V, Zn) Levels in Sarpa Salpa from the North-Eastern Atlantic Ocean Region

Sarpa salpa is a fish belonging to the Sparidae family and is usually found in local markets. Toxic metals such as aluminum (Al), cadmium (Cd), lead (Pb) and trace elements such as boron (B), barium (Ba), cobalt (Co), copper (Cu), chromium (Cr), iron (Fe), lithium (Li), manganese (Mn), molybdenum (Mo), nickel (Ni), strontium (Sr), vanadium (V) and zinc (Zn) are incorporated into fish tissues and remain there. The liver has the highest concentrations of all the analyzed toxic metals and almost all the analyzed trace elements. The consumption of 100 g/day of S. salpa muscle tissue does not pose a health risk. However, 100 g/day of liver consumption may pose a serious health risk due to the intake of Cd (572% of the tolerable weekly intake for adults with a body weight of 68.48 kg) and Pb (117% of the tolerable daily intake for adults weighing 68.48 kg). The consumption of liver of this species is not recommended due to its possible harmful effects on health.
Small Ruminant Production Based on Rangelands to Optimize Animal Nutrition and Health: Building an Interdisciplinary Approach to Evaluate Nutraceutical Plants

Simple Summary The low deciduous forest is an ecosystem covering 8% of México’s surface and is present in 15 of the 32 states of the country. It has been observed that sheep and goats feeding in this high biodiverse biome can consume up to 80 plant species. In addition, the low deciduous forest biomass is frequently used to feed small ruminants in cut and carry systems. However, there is not enough information to provide guidelines for its sustainable use by ruminant livestock. In the present review, we present an interdisciplinary approach aimed at identifying the nutraceutical properties of this native vegetation system, involving disciplines like botany, ecology, agronomy, ethology, ethnoveterinary, nutrition, parasitology and chemistry. Nutraceuticals are defined as livestock feeds combining nutritional value with beneficial effects on animal health and productivity. The identification of nutraceutical properties amongst plant species of the low deciduous forest may contribute to the revalorization of this native vegetation system and provide information enabling the design of sustainable livestock feeding/management systems that benefit the nutrition and health of small ruminants, and ultimately human health through the consumption of animal products produced in this native vegetation system. Abstract The plant kingdom can influence the productivity and health of herbivores at different levels. However, demonstrating this process in a scientific manner entails substantial endeavors from different disciplines. In the present review, we will describe the features of a native vegetation system traditionally used by small ruminants and use its particularities to build an interdisciplinary approach to evaluate the nutraceutical properties of plants. Initially, we will establish the context of the low deciduous forest (LDF), considering some botanical and nutritional aspects, as well as the presence of plant secondary compounds (PSC) and gastrointestinal nematodes (GIN). Furthermore, we will focus on coevolutionary aspects that undoubtedly shaped the plants–nutrients–PSC–GIN–herbivore relationship. In addition, the concept of nutraceutical will be discussed to provide clarity and aspects to be considered for their evaluation. Then, ethological, agronomical, nutritional, PSC, parasitological and animal species issues are deepened placing emphasis on methodological approaches. Special focus is given to condensed tannins, as they are the fourth largest group of PSCs and the most studied in livestock sciences. Validation of the nutraceutical properties of plants from native vegetation systems should be seen as a process derived from many scientific disciplines that feed into each other in a cyclic manner.